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| Skeletal dysplasia v0.289 | DDX41 |
Chirag Patel gene: DDX41 was added gene: DDX41 was added to Skeletal dysplasia. Sources: Literature Mode of inheritance for gene: DDX41 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: DDX41 were set to PMID: 39453476 Phenotypes for gene: DDX41 were set to Bone dysplasia, ichthyosis, and dysmorphism Review for gene: DDX41 was set to RED Added comment: 1 patient with acromesomelic dysplasia (short stature, premature closure of epiphyses of hands/feet), chronic ichthyotic-like skin changes, joint pain, facial dysmorphism, dental crowding, difficulty in swallowing, hyperinsulinism, and absent breast development.. WES identified compound heterozygous DDX41 variants (p.Met155Ile and p.Glu345Lys). Parents confirmed carriers of single variant. DDX41 (DEAD‑box helicase 41) is a member of the largest family of RNA helicases. The DEAD-box RNA helicases regulate all aspects of RNA metabolism. DDX41 acts as a sensor of viral DNA and activates the STING-TBK1-IRF3-type I IFN signaling pathway. Functional analyses of the patient-derived dermal fibroblasts revealed a reduced abundance of DDX41 and abrogated activation of the IFN genes through the STING-type I interferon pathway. Genome-wide transcriptome analyses in the patient's fibroblasts revealed significant gene dysregulation and changes in the RNA splicing events. The patient's fibroblasts also displayed upregulation of periostin mRNA expression. Using an RNA binding protein assay, they identified DDX41 as a novel regulator of periostin expression. Sources: Literature |
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| Skeletal dysplasia v0.280 | PISD | Zornitza Stark Phenotypes for gene: PISD were changed from Liberfarb syndrome MIM# 618889; Spondylometaphyseal dysplasia with large epiphyses to Liberfarb syndrome MIM# 618889; Spondylometaphyseal dysplasia with large epiphyses, MONDO:0100510 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.279 | PISD | Zornitza Stark Phenotypes for gene: PISD were changed from Spondylometaphyseal dysplasia with large epiphyses to Liberfarb syndrome MIM# 618889; Spondylometaphyseal dysplasia with large epiphyses | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.277 | PISD | Sangavi Sivagnanasundram reviewed gene: PISD: Rating: GREEN; Mode of pathogenicity: None; Publications: 38801004; Phenotypes: Liberfarb syndrome MONDO:0030045; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.243 | DDRGK1 | Ain Roesley Added comment: Comment when marking as ready: RNA and protein studies performed for the splice variant. These two variants likely represents founder variants | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.209 | ALPL | Zornitza Stark Phenotypes for gene: ALPL were changed from hypophosphatasia; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias to Hypophosphatasia, adult 146300 (AD, AR); Hypophosphatasia, childhood 241510 AR; Hypophosphatasia, infantile 241500 AR; Odontohypophosphatasia 146300 AD, AR | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.150 | SMAD6 |
Chris Richmond gene: SMAD6 was added gene: SMAD6 was added to Skeletal dysplasia. Sources: Expert Review Mode of inheritance for gene: SMAD6 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: SMAD6 were set to 31138930 Phenotypes for gene: SMAD6 were set to 179300 Penetrance for gene: SMAD6 were set to Incomplete Review for gene: SMAD6 was set to GREEN gene: SMAD6 was marked as current diagnostic Added comment: Yang et al. (2019) performed exome sequencing on 117 patients with sporadic RUS and found significant enrichment for loss-of-function variants in the SMAD6 gene. Identified 22 SMAD6 rare variants (with a minor allele frequency of less than 0.0001) that occurred in 22 nonsyndromic RUS patients. Logistic regression showed that SMAD6 loss-of-function variants were significantly associated with increased risk of nonsyndromic RUS (OR 430; 95% CI 237.5-780.1; p less than 0.000001). Some inherited from unaffected parents. Sources: Expert Review |
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| Skeletal dysplasia v0.137 | IFITM5 | Seb Lunke Phenotypes for gene: IFITM5 were changed from Osteogenesis imperfecta, type V 610967 to Osteogenesis imperfecta, type V MIM#610967 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.135 | IFITM5 | Ain Roesley reviewed gene: IFITM5: Rating: GREEN; Mode of pathogenicity: None; Publications: 22863190, 22863195, 32383316, 24519609; Phenotypes: Osteogenesis imperfecta, type V MIM#610967; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted; Current diagnostic: yes | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Skeletal dysplasia v0.89 | MIA3 |
Zornitza Stark gene: MIA3 was added gene: MIA3 was added to Skeletal dysplasia. Sources: Expert list Mode of inheritance for gene: MIA3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MIA3 were set to 32101163; 33778321 Phenotypes for gene: MIA3 were set to Ondontochondrodysplasia 2 with hearing loss and diabetes , MIM#619269 Review for gene: MIA3 was set to AMBER Added comment: Odontochondrodysplasia-2 with hearing loss and diabetes (ODCD2) is characterized by growth retardation with proportionate short stature, dentinogenesis imperfecta, sensorineural hearing loss, insulin-dependent diabetes, and mild intellectual disability. Four affected siblings reported, homozygous variant affecting splicing. Mouse model has absence of bone mineralization. Sources: Expert list |
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| Skeletal dysplasia v0.76 | TMEM251 |
Bryony Thompson gene: TMEM251 was added gene: TMEM251 was added to Skeletal dysplasia. Sources: Literature Mode of inheritance for gene: TMEM251 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TMEM251 were set to 33252156 Phenotypes for gene: TMEM251 were set to Dysostosis multiplex‐like skeletal dysplasia; severe short stature Review for gene: TMEM251 was set to AMBER Added comment: Two unrelated consanguineous families with homozygous variants (c.133C>T; p.Arg45Trp and c.215dupA; p.Tyr72Ter), with co-segregation data in one family. Preliminary in vitro functional assays conducted - Tmem251 knockdown by small interfering RNA induced dedifferentiation of rat primary chondrocytes. Sources: Literature |
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| Skeletal dysplasia v0.4 | MESD |
Zornitza Stark gene: MESD was added gene: MESD was added to Skeletal dysplasia. Sources: Other Mode of inheritance for gene: MESD was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: MESD were set to 31564437 Phenotypes for gene: MESD were set to Osteogenesis imperfecta, type XX, MIM# 618644 Review for gene: MESD was set to GREEN Added comment: Five unrelated families reported. Sources: Other |
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| Skeletal dysplasia v0.0 | TDP2 |
Zornitza Stark gene: TDP2 was added gene: TDP2 was added to Skeletal dysplasia. Sources: Expert Review Red,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: TDP2 was set to Phenotypes for gene: TDP2 were set to Dentinogenesis imperfecta, Shields type II, 125490 |
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| Skeletal dysplasia v0.0 | WNT1 |
Zornitza Stark gene: WNT1 was added gene: WNT1 was added to Skeletal dysplasia. Sources: NHS GMS,Radboud University Medical Center, Nijmegen,Expert,Expert Review Green Mode of inheritance for gene: WNT1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: WNT1 were set to OI/osteoporosis; osteogenesis imperfecta; Osteogenesis imperfecta, type XV, 615220; {Osteoporosis, early-onset, susceptibility to, autosomal dominant}, 615221 |
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| Skeletal dysplasia v0.0 | TMEM38B |
Zornitza Stark gene: TMEM38B was added gene: TMEM38B was added to Skeletal dysplasia. Sources: NHS GMS,Radboud University Medical Center, Nijmegen,Expert,Expert Review Green Mode of inheritance for gene: TMEM38B was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: TMEM38B were set to Osteogenesis imperfecta, type XIV 615066; osteogenesis imperfecta; Osteogenesis imperfecta, type XIV, 615066 |
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| Skeletal dysplasia v0.0 | SPARC |
Zornitza Stark gene: SPARC was added gene: SPARC was added to Skeletal dysplasia. Sources: Expert list,Expert Review Green Mode of inheritance for gene: SPARC was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SPARC were set to 26027498 Phenotypes for gene: SPARC were set to Osteogenesis imperfecta, type XVII 616507 |
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| Skeletal dysplasia v0.0 | SP7 |
Zornitza Stark gene: SP7 was added gene: SP7 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green,Radboud University Medical Center, Nijmegen,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: SP7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SP7 were set to 29382611; 2057926 Phenotypes for gene: SP7 were set to Osteogenesis imperfecta, type XII 613849 |
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| Skeletal dysplasia v0.0 | SLC10A7 |
Zornitza Stark gene: SLC10A7 was added gene: SLC10A7 was added to Skeletal dysplasia. Sources: Literature,Expert Review Green Mode of inheritance for gene: SLC10A7 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC10A7 were set to 30082715 Phenotypes for gene: SLC10A7 were set to skeletal dysplasia and amelogenesis imperfecta; Short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis 618363 |
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| Skeletal dysplasia v0.0 | SERPINH1 |
Zornitza Stark gene: SERPINH1 was added gene: SERPINH1 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green,Radboud University Medical Center, Nijmegen,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: SERPINH1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SERPINH1 were set to 20188343; 25510505 Phenotypes for gene: SERPINH1 were set to Osteogenesis imperfecta, type X, 613848; OI3; Osteogenesis Imperfecta and Decreased Bone Density; {Preterm premature rupture of the membranes, susceptibility to}, 610504; skeletal dysplasias; Osteogenesis Imperfecta, Recessive |
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| Skeletal dysplasia v0.0 | SERPINF1 |
Zornitza Stark gene: SERPINF1 was added gene: SERPINF1 was added to Skeletal dysplasia. Sources: NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: SERPINF1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SERPINF1 were set to OI/osteoporosis; osteogenesis imperfecta; Osteogenesis Imperfecta, Recessive; Osteogenesis imperfecta, type VI, 613982 |
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| Skeletal dysplasia v0.0 | SEC24D |
Zornitza Stark gene: SEC24D was added gene: SEC24D was added to Skeletal dysplasia. Sources: NHS GMS,Literature,Expert Review,Expert Review Green Mode of inheritance for gene: SEC24D was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SEC24D were set to 25683121 Phenotypes for gene: SEC24D were set to Cole-Carpenter syndrome; SYNDROMIC OSTEOGENESIS IMPERFECTA; Osteogenesis Imperfecta, Cole Carpenter syndrome |
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| Skeletal dysplasia v0.0 | PPIB |
Zornitza Stark gene: PPIB was added gene: PPIB was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green,Radboud University Medical Center, Nijmegen,UKGTN,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: PPIB was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: PPIB were set to Osteogenesis imperfecta, type IX 259440; Osteogenesis imperfecta, type IX 259440 |
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| Skeletal dysplasia v0.0 | P3H1 |
Zornitza Stark gene: P3H1 was added gene: P3H1 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,Expert list,NHS GMS,Expert Review Green,UKGTN Mode of inheritance for gene: P3H1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: P3H1 were set to Osteogenesis imperfecta, type VIII 610915 |
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| Skeletal dysplasia v0.0 | IFITM5 |
Zornitza Stark gene: IFITM5 was added gene: IFITM5 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,Eligibility statement prior genetic testing Mode of inheritance for gene: IFITM5 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: IFITM5 were set to Osteogenesis imperfecta, type V 610967 |
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| Skeletal dysplasia v0.0 | FKBP10 |
Zornitza Stark gene: FKBP10 was added gene: FKBP10 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: FKBP10 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: FKBP10 were set to Osteogenesis imperfecta, type XI, 610968; Brucks syndrome 1 - 259450; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias; Osteogenesis Imperfecta, Recessive; Brucks syndrome |
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| Skeletal dysplasia v0.0 | FAM46A |
Zornitza Stark gene: FAM46A was added gene: FAM46A was added to Skeletal dysplasia. Sources: Other,Expert Review Green Mode of inheritance for gene: FAM46A was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: FAM46A were set to 29358272 Phenotypes for gene: FAM46A were set to Osteogenesis imperfecta, type XVIII 617952 |
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| Skeletal dysplasia v0.0 | ERF |
Zornitza Stark gene: ERF was added gene: ERF was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,Expert list,NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,UKGTN Mode of inheritance for gene: ERF was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ERF were set to 23354439; 26097063 Phenotypes for gene: ERF were set to Craniosynostosis 4 600775; Chitayat syndrome - 617180 |
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| Skeletal dysplasia v0.0 | DSPP |
Zornitza Stark gene: DSPP was added gene: DSPP was added to Skeletal dysplasia. Sources: Radboud University Medical Center, Nijmegen,Expert Review Green Mode of inheritance for gene: DSPP was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DSPP were set to 27973701; 29512331 Phenotypes for gene: DSPP were set to Dentin dysplasia, type II, 125420 -3; Dentinogenesis imperfecta, Shields type III, 125500; Dentinogenesis imperfecta, Shields type II, 125490; Deafness, autosomal dominant 36, with dentinogenesis, 605594 |
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| Skeletal dysplasia v0.0 | DMP1 |
Zornitza Stark gene: DMP1 was added gene: DMP1 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,Expert Mode of inheritance for gene: DMP1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: DMP1 were set to Acromesomelic dysplasia, Hunter-Thompson type, 201250; Symphalangism, proximal, 1B, 615298; Hypophosphatemic rickets,autosomal recessive,type 1 (ARHR1); Brachydactyly, type A1, C, 615072; Brachydactyly, type A2, 112600; Du Pan syndrome, 228900; Hypophosphatemic rickets, AR, 241520; Osteogenesis Imperfecta and Decreased Bone Density; Chondrodysplasia, Grebe type, 200700; skeletal dysplasias; Brachydactyly, type C, 113100; {Osteoarthritis-5}, 612400; Multiple synostoses syndrome 2, 610017 |
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| Skeletal dysplasia v0.0 | DLX3 |
Zornitza Stark gene: DLX3 was added gene: DLX3 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,Expert list,NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,UKGTN Mode of inheritance for gene: DLX3 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: DLX3 were set to 26762616; 26104267 Phenotypes for gene: DLX3 were set to Trichodontoosseous syndrome 190320; Amelogenesis imperfecta, type IV 104510 |
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| Skeletal dysplasia v0.0 | CRTAP |
Zornitza Stark gene: CRTAP was added gene: CRTAP was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green,Radboud University Medical Center, Nijmegen,UKGTN,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: CRTAP was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: CRTAP were set to Osteogenesis imperfecta, type VII 610682 |
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| Skeletal dysplasia v0.0 | CREB3L1 |
Zornitza Stark gene: CREB3L1 was added gene: CREB3L1 was added to Skeletal dysplasia. Sources: NHS GMS,Literature,Expert Review,Expert Review Green Mode of inheritance for gene: CREB3L1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: CREB3L1 were set to 25007323; 28817112; 29936144.; 30657919 Phenotypes for gene: CREB3L1 were set to Osteogenesis imperfecta, type XVI 616229 |
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| Skeletal dysplasia v0.0 | COL1A2 |
Zornitza Stark gene: COL1A2 was added gene: COL1A2 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green,Radboud University Medical Center, Nijmegen,Eligibility statement prior genetic testing,UKGTN,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: COL1A2 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Phenotypes for gene: COL1A2 were set to Osteogenesis imperfecta, type III 259420; Osteogenesis imperfecta, type IV 166220; Ehlers-Danlos syndrome, type VIIB 130060; Ehlers-Danlos syndrome, cardiac valvular form 225320; Osteogenesis imperfecta, type II 166210 |
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| Skeletal dysplasia v0.0 | COL1A1 |
Zornitza Stark gene: COL1A1 was added gene: COL1A1 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green,Radboud University Medical Center, Nijmegen,Eligibility statement prior genetic testing,UKGTN,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: COL1A1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: COL1A1 were set to Ehlers-Danlos syndrome, type VIIA 130060; Osteogenesis imperfecta, type III 259420; Osteogenesis imperfecta, type I 166200; Osteogenesis imperfecta, type IV 166220; Ehlers-Danlos syndrome, classic 130000; Caffey disease 114000; Osteogenesis imperfecta, type II 166210 |
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| Skeletal dysplasia v0.0 | BMP1 |
Zornitza Stark gene: BMP1 was added gene: BMP1 was added to Skeletal dysplasia. Sources: NHS GMS,Radboud University Medical Center, Nijmegen,Expert Review Green,Expert,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: BMP1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: BMP1 were set to Osteogenesis imperfecta, type XIII, 614856 |
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| Skeletal dysplasia v0.0 | ANO5 |
Zornitza Stark gene: ANO5 was added gene: ANO5 was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green Mode of inheritance for gene: ANO5 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: ANO5 were set to Disproportionate Short Stature; Osteogenesis Imperfecta and Decreased Bone Density; Gnatodiaphyseal dysplasia; skeletal dysplasias |
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| Skeletal dysplasia v0.0 | ALPL |
Zornitza Stark gene: ALPL was added gene: ALPL was added to Skeletal dysplasia. Sources: Emory Genetics Laboratory,NHS GMS,Expert Review Green Mode of inheritance for gene: ALPL was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal Phenotypes for gene: ALPL were set to hypophosphatasia; Osteogenesis Imperfecta and Decreased Bone Density; skeletal dysplasias |
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