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Fetal anomalies v1.587 PLAT Zornitza Stark Marked gene: PLAT as ready
Fetal anomalies v1.587 PLAT Zornitza Stark Gene: plat has been classified as Green List (High Evidence).
Fetal anomalies v1.587 PLAT Zornitza Stark Phenotypes for gene: PLAT were changed from Syndromic disease, MONDO:0002254, PLAT-related; Thrombophilia, familial, due to decreased release of tissue plasminogen activator MONDO:0012872 to Syndromic disease, MONDO:0002254, PLAT-related
Fetal anomalies v1.586 PLAT Zornitza Stark Tag disputed was removed from gene: PLAT.
Fetal anomalies v1.586 Zornitza Stark Copied gene PLAT from panel Mendeliome
Fetal anomalies v1.586 PLAT Zornitza Stark gene: PLAT was added
gene: PLAT was added to Fetal anomalies. Sources: Expert Review Green,ClinGen,ClinGen
disputed tags were added to gene: PLAT.
Mode of inheritance for gene: PLAT was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: PLAT were set to 39574431; 37808270; 27417437
Phenotypes for gene: PLAT were set to Syndromic disease, MONDO:0002254, PLAT-related; Thrombophilia, familial, due to decreased release of tissue plasminogen activator MONDO:0012872
Fetal anomalies v1.476 COL10A1 Zornitza Stark changed review comment from: Note: Gene reviews also notes severe lethal phenotypes in recessive inheritance where parents were only mildly affected, however only 2 unrelated families reported to date (PMID: 31633898). Both haploinsufficiency and dominant-negative mechanisms have been suggested to cause disease (OMIM, PMID: 15880705, PMID: 31633898). “Pathogenic variants in COL10A1 are clustered in the C-terminal non-collagenous (NC1) domain, which contains motifs required for normal assembly of the collagen trimer. Both missense and truncating (frameshift and nonsense) variants in COL10A1 cause collagen X protein misfolding during protein synthesis, resulting in a failure of trimerization and aggregation within the endoplasmic reticulum (ER) of hypertrophic chondrocytes. Resultant ER stress, activation of the unfolded protein response, and reduced levels of functional type X collagen in the growth plate cause chondrodysplasia and development of the SMCD phenotype [Rajpar et al 2009].” -> from Gene Reviews (PMID: 31633898). Some pathogenic missense also reported in the N-terminal signal peptide (Decipher), however please note that to date, no Gly-X-Y substitutions in the collagen triple helix repeats have yet been reported, pathogenic or otherwise.; to: Note: Gene reviews also notes severe lethal phenotypes in recessive inheritance where parents were only mildly affected, however only 2 unrelated families reported to date (PMID: 31633898). Both haploinsufficiency and dominant-negative mechanisms have been suggested to cause disease (OMIM, PMID: 15880705, PMID: 31633898). “Pathogenic variants in COL10A1 are clustered in the C-terminal non-collagenous (NC1) domain, which contains motifs required for normal assembly of the collagen trimer. Both missense and truncating (frameshift and nonsense) variants in COL10A1 cause collagen X protein misfolding during protein synthesis, resulting in a failure of trimerization and aggregation within the endoplasmic reticulum (ER) of hypertrophic chondrocytes. Resultant ER stress, activation of the unfolded protein response, and reduced levels of functional type X collagen in the growth plate cause chondrodysplasia and development of the SMCD phenotype [Rajpar et al 2009].” -> from Gene Reviews (PMID: 31633898). Some pathogenic missense also reported in the N-terminal signal peptide (Decipher).

Note that unlike with other collagens, Gly-X-Y substitutions in the collagen triple helix repeats are very rarely reported as disease-causing, and may result in a milder phenotype (PMID 31348255; 25542771). These should be interpreted with caution.
Fetal anomalies v1.120 ERI1 Zornitza Stark gene: ERI1 was added
gene: ERI1 was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: ERI1 was set to BOTH monoallelic and biallelic (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal
Publications for gene: ERI1 were set to 37352860
Phenotypes for gene: ERI1 were set to Spondyloepimetaphyseal dysplasia (MONDO#0100510)
Review for gene: ERI1 was set to GREEN
Added comment: PMID: 37352860 - 8 individuals from 7 unrelated families
- Patients with biallelic missense show a MORE severe spondyloepimetaphyseal dysplasia, syndactyly, brachydactyly/clinodactyly/camptodactyly
- Patients with biallelic null/whole gene deletion had mild ID and digit anomalies including brachydactyly/clinodactyly/camptodactyly
- Patient chet for a missense and PTC variant has a blended phenotype with short stature, syndactyly, brachydactyly/clinodactyly/camptodactyly, mild ID and failure to thrive

- Missense variants were functionally shown to not be able to rescue 5.8S rRNA processing in KO HeLa cells
- K/O mice had neonatal lethality with growth defects, brachydactyly. Skeletal-specific K/O had mild platyspondyly, had more in keeping with patients with null variants than missense

More severe phenotype hypothesised due to "exonuclease-dead proteins may compete for the target RNA molecules with other exonucleases that have functional redundancy
with ERI1, staying bound to those RNA molecules"
Sources: Literature
Fetal anomalies v1.58 KIF5B Chirag Patel gene: KIF5B was added
gene: KIF5B was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: KIF5B was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: KIF5B were set to PMID: 35342932
Phenotypes for gene: KIF5B were set to Kyphomelic dysplasia, no OMIM #
Review for gene: KIF5B was set to GREEN
Added comment: 4 individuals with Kyphomelic dysplasia (severe bowing of the limbs, sharp angulation of the femora and humeri, short stature, narrow thorax, distinctive facial features, and neonatal respiratory distress. WES found de novo heterozygous missense variants in KIF5B encoding kinesin-1 heavy chain. All variants involved conserved amino acids in or close to the ATPase activity-related motifs in the catalytic motor domain of the KIF5B protein. No functional studies of variants.

Previously 2 animal model experiments showed that loss of function of KIF5B can cause kyphomelic dysplasia. First, chondrocyte-specific knockout of Kif5b in mice was shown to produce a disorganized growth plate, leading to bone deformity. Second, double mutants disrupting the two zebrafish kif5b caused abnormal skeletal morphogenesis and the curvature of Meckel's and ceratohyal cartilages.
Sources: Literature
Fetal anomalies v0.4198 RASGRP2 Zornitza Stark Phenotypes for gene: RASGRP2 were changed from ?Bleeding disorder, platelet-type, 18 - MIM#615888 to Bleeding disorder, platelet-type, 18 - MIM#615888
Fetal anomalies v0.4132 RASGRP2 Krithika Murali gene: RASGRP2 was added
gene: RASGRP2 was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: RASGRP2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: RASGRP2 were set to 28637664; 28726538; 28762304; 30046681; 34066320; 33711653; 33376940; 32609603; 30849270; 30046681
Phenotypes for gene: RASGRP2 were set to ?Bleeding disorder, platelet-type, 18 - MIM#615888
Review for gene: RASGRP2 was set to RED
Added comment: Postnatal presentation only with no antenatal features reported.
Sources: Literature
Fetal anomalies v0.4132 FERMT3 Krithika Murali gene: FERMT3 was added
gene: FERMT3 was added to Fetal anomalies. Sources: Literature
Mode of inheritance for gene: FERMT3 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: FERMT3 were set to 31068971; 34485203; 33391282; 31724816; 30412664; 25854317; 28095295; 26359933; 25072369; 22134107; 20216991; 19234463; 19234460; 18779414
Phenotypes for gene: FERMT3 were set to Leukocyte adhesion deficiency, type III - MIM#612840
Review for gene: FERMT3 was set to RED
Added comment: Biallelic variants associated with LAD3 syndrome (primary immunodeficiency and platelet function defects). Symptom onset reported from birth, no antenatal features reported.

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PMID: 34485203 Yahya et al 2021 - no antenatal issues reported

PMID: 33391282 Kambli et al 2020 - no antenatal features reported for 5 individuals with LAD3

PMID 31068971 Shahid et al 2019 - no antenatal features

PMID: 31724816 Manukjan et al 2019 - no antenatal issues reported in 1 affected individual

PMID: 28095295 Palagano et al 2017 - report female proband with infantile-onset osteopetrosis and symptomatic haematological anomalies at birth requiring bone marrow transplant. Authors postulate in utero onset but no antenatal features reported.

PMID: 26359933 Suratannon et al 2016 - report a female Thai proband with a milder/atypical phenotype, no antenatal features reported

PMID: 25854317 Crazzolara et al 2015 - presented D7 of life with infection, bleeeding issues and noted radiologically to have dense bones. No antenatal features.

PMID: 25072369 Stepensky et al 2015 - report 3 individuals with bleeding tendency from birth and onset of recurrent infections as an infant, normal antenatal history.

PMID: 20357244 McDowall et al 2010 - symptom onset from birth, no antenatal features

PMID: 20216991 Jurk et al 2010 - 2 affected siblings, no antenatal features reported.

PMID: 19234463 Svensson et al 2009 - no antenatal features reported

PMID: 19234460 Malinin et al 2009 - no antenatal features reported

PMID: 19064721 Kuijpers et al 2009 - 9 individuals from 7 unrelated families, no antenatal features reported.
Sources: Literature
Fetal anomalies v0.1114 BLOC1S6 Zornitza Stark changed review comment from: Same homozygous variant identified in two individuals with HPS, however, note that one of the articles has been retracted due to some of the data having been falsified. Another individual reported in 32245340 but pigmentary and platelet abnormalities only.

Presentation for HPS in general is post-natal.; to: Same homozygous variant identified in two individuals with HPS, however, note that one of the articles has been retracted due to some of the data having been falsified. Another individual reported in 32245340 but pigmentary and platelet abnormalities only.

Presentation of HPS in general is post-natal.
Fetal anomalies v0.1104 B9D1 Zornitza Stark edited their review of gene: B9D1: Added comment: 3 unrelated cases with a syndromic phenotype and a supporting null mouse model
PMID: 34338422 - compound het missense and frameshift variant in a proband with anal atresia with vestibular fistula, ventricular septal defect, and right renal agenesis (VACTERL cohort)
PMID: 24886560 - 2 Joubert syndrome cases
PMID: 21763481 - B9d1 -/- mouse displayed polydactyly, kidney cysts, ductal plate malformations, and abnormal patterning of the neural tube, concomitant with compromised ciliogenesis, ciliary protein localization, and Hedgehog (Hh) signal transduction.; Changed rating: GREEN
Fetal anomalies v0.1081 DYM Zornitza Stark changed review comment from: Dyggve-Melchior-Clausen disease (DMC) is an autosomal recessive disorder characterized by progressive spondyloepimetaphyseal dysplasia and impaired intellectual development. Short-trunk dwarfism and microcephaly are present, and specific radiologic appearances most likely reflect abnormalities of the growth plates, including platyspondyly with notched end plates, metaphyseal irregularities, laterally displaced capital femoral epiphyses, and small iliac wings with lacy iliac crests. More than 5 untreated families reported.; to: Dyggve-Melchior-Clausen disease (DMC) is an autosomal recessive disorder characterized by progressive spondyloepimetaphyseal dysplasia and impaired intellectual development. Short-trunk dwarfism and microcephaly are present, and specific radiologic appearances most likely reflect abnormalities of the growth plates, including platyspondyly with notched end plates, metaphyseal irregularities, laterally displaced capital femoral epiphyses, and small iliac wings with lacy iliac crests. More than 5 untreated families reported.

Smith-McCort dysplasia is a rare autosomal recessive osteochondrodysplasia characterized by short limbs and trunk with barrel-shaped chest. The radiographic phenotype includes platyspondyly, generalized abnormalities of the epiphyses and metaphyses, and a distinctive lacy appearance of the iliac crest, features identical to those of Dyggve-Melchior-Clausen disease.

The two conditions likely represent a spectrum rather than two distinct disorders.
Fetal anomalies v0.1081 DYM Zornitza Stark changed review comment from: Dyggve-Melchior-Clausen disease (DMC) is an autosomal recessive disorder characterized by progressive spondyloepimetaphyseal dysplasia and impaired intellectual development. Short-trunk dwarfism and microcephaly are present, and specific radiologic appearances most likely reflect abnormalities of the growth plates, including platyspondyly with notched end plates, metaphyseal irregularities, laterally displaced capital femoral epiphyses, and small iliac wings with lacy iliac crests; to: Dyggve-Melchior-Clausen disease (DMC) is an autosomal recessive disorder characterized by progressive spondyloepimetaphyseal dysplasia and impaired intellectual development. Short-trunk dwarfism and microcephaly are present, and specific radiologic appearances most likely reflect abnormalities of the growth plates, including platyspondyly with notched end plates, metaphyseal irregularities, laterally displaced capital femoral epiphyses, and small iliac wings with lacy iliac crests. More than 5 untreated families reported.
Fetal anomalies v0.1081 DYM Zornitza Stark commented on gene: DYM: Dyggve-Melchior-Clausen disease (DMC) is an autosomal recessive disorder characterized by progressive spondyloepimetaphyseal dysplasia and impaired intellectual development. Short-trunk dwarfism and microcephaly are present, and specific radiologic appearances most likely reflect abnormalities of the growth plates, including platyspondyly with notched end plates, metaphyseal irregularities, laterally displaced capital femoral epiphyses, and small iliac wings with lacy iliac crests
Fetal anomalies v0.737 PPIB Naomi Baker changed review comment from: Well established gene-disease association with lethal or severe phenotype.

PMID: 19781681; reported biallelic loss-of-function variants in two consanguineous families. Multiple skeletal features were observed in fetal radiographs, including fractures of long bones, bowed tibiae, fibula and femora, and beaded ribs.

PMID: 32392875; reported an identical biallelic missense variant in two Taiwanese families. Prenatal imaging showed small and collapsed thoracic cage, bowing of femoral bone, and platyspondyly of spine.; to: Well established gene-disease association with lethal or severe OI phenotype.

PMID: 19781681; reported biallelic loss-of-function variants in two consanguineous families. Multiple skeletal features were observed in fetal radiographs, including fractures of long bones, bowed tibiae, fibula and femora, and beaded ribs.

PMID: 32392875; reported an identical biallelic missense variant in two Taiwanese families. Prenatal imaging showed small and collapsed thoracic cage, bowing of femoral bone, and platyspondyly of spine.
Fetal anomalies v0.675 GATA1 Zornitza Stark Phenotypes for gene: GATA1 were changed from Anaemia, X-linked, with/without neutropenia and/or platelet abnormalities, MIM#300835 to Anaemia, X-linked, with/without neutropaenia and/or platelet abnormalities, MIM#300835
Fetal anomalies v0.674 GATA1 Zornitza Stark Phenotypes for gene: GATA1 were changed from Anemia, X-linked, with/without neutropenia and/or platelet abnormalities, MIM#300835 to Anaemia, X-linked, with/without neutropenia and/or platelet abnormalities, MIM#300835
Fetal anomalies v0.637 GATA1 Krithika Murali gene: GATA1 was added
gene: GATA1 was added to Fetal anomalies. Sources: Expert list
Mode of inheritance for gene: GATA1 was set to X-LINKED: hemizygous mutation in males, biallelic mutations in females
Publications for gene: GATA1 were set to 10700180
Phenotypes for gene: GATA1 were set to Anemia, X-linked, with/without neutropenia and/or platelet abnormalities, MIM#300835
Review for gene: GATA1 was set to GREEN
Added comment: Can present with severe hydrops in utero requiring transfusion.
Sources: Expert list
Fetal anomalies v0.573 COL2A1 Zornitza Stark Phenotypes for gene: COL2A1 were changed from KNIEST DYSPLASIA; SPONDYLOEPIMETAPHYSEAL DYSPLASIA STRUDWICK TYPE; PLATYSPONDYLIC LETHAL SKELETAL DYSPLASIA TORRANCE TYPE; STICKLER SYNDROME TYPE 1 NON-SYNDROMIC OCULAR; RHEGMATOGENOUS RETINAL DETACHMENT AUTOSOMAL DOMINANT; SPONDYLOEPIPHYSEAL DYSPLASIA CONGENITA; ACHONDROGENESIS TYPE 2; SPONDYLOPERIPHERAL DYSPLASIA to Collagenopathy type 2 alpha 1, MONDO:0022800
Fetal anomalies v0.453 LTBP3 Zornitza Stark Phenotypes for gene: LTBP3 were changed from PLATYSPONDYLY WITH AMELOGENESIS IMPERFECTA to Dental anomalies and short stature, MIM# 601216; Geleophysic dysplasia 3, MIM# 617809; Thoracic aneurysm
Fetal anomalies v0.0 LTBP3 Zornitza Stark gene: LTBP3 was added
gene: LTBP3 was added to Fetal anomalies. Sources: Expert Review Green,Genomics England PanelApp
Mode of inheritance for gene: LTBP3 was set to BIALLELIC, autosomal or pseudoautosomal
Phenotypes for gene: LTBP3 were set to PLATYSPONDYLY WITH AMELOGENESIS IMPERFECTA
Fetal anomalies v0.0 COL2A1 Zornitza Stark gene: COL2A1 was added
gene: COL2A1 was added to Fetal anomalies. Sources: Expert Review Green,Genomics England PanelApp
Mode of inheritance for gene: COL2A1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes for gene: COL2A1 were set to KNIEST DYSPLASIA; SPONDYLOEPIMETAPHYSEAL DYSPLASIA STRUDWICK TYPE; PLATYSPONDYLIC LETHAL SKELETAL DYSPLASIA TORRANCE TYPE; STICKLER SYNDROME TYPE 1 NON-SYNDROMIC OCULAR; RHEGMATOGENOUS RETINAL DETACHMENT AUTOSOMAL DOMINANT; SPONDYLOEPIPHYSEAL DYSPLASIA CONGENITA; ACHONDROGENESIS TYPE 2; SPONDYLOPERIPHERAL DYSPLASIA