Mendeliome
Gene: KLF13 Amber List (moderate evidence)Comment on publications: Publications weren't updated at the time of review - no new evidence has been reported.Created: 8 Apr 2026, 11:57 a.m. | Last Modified: 8 Apr 2026, 11:57 a.m.
Panel Version: 1.4732
I don't know
Curated by ClinGen as Moderate for association with congenital heart disease (12/2/2024)
PMID: 33215447 Wang et al 2020 - novel heterozygous variation, NM_015995.3: c.370G>T; p.(Glu124*), co-segregating with congenital heart disease in a 3-generation Chinese family. Supportive functional evidence.
PMID: 35369534 Abhinav et al 2022 - NM_015995.3: c.430G>T; p.(Glu144*) co-segregated with congenital heart disease in a Han Chinese family. Supportive functional evidence.
PMID: 32293321 Li et al 2020 - Two heterozygous missense variants in two unrelated patients with congenital heart disease. However, they have much higher gnomAD frequencies - c.487C > T (P163S) (11 hets gnomAD v4) and c.467G > A (S156N)(22 hets gnomAD v4). No segregation information and the functional evidence was not convincing. This paper was included as genetic evidence in the ClinGen curation.
Monoallelic variants have also been reported in association with adult-onset DCM.
PMID 36346048 Guo et al 2022 – Identified heterozygous KLF13 gene variants co-segregating with adult-onset DCM in 3 unrelated families - c.430G>T (p.E144X); c.580G>T (p.E194X) and c.595T>C (p.C199R). Functional studies support disrupted synergistic transactivation between mutant KLF13 and target genes ACTC1, MYH7 and GATA4. Monoallelic variants in KLF13 have also been associated with congenital heart disease. Of note, 2 individuals from Family 1 and 1 individual from Family 2 also had an atrial septal defect.
PMID 41201692 Tang et al 2025 – report a novel heterozygous truncating KLF13 mutation, i.e., NM_015995.3:c.534 C>G;p.(Tyr178) in two unrelated patients with adult onset DCM (42-year-old male patient and a 51-year old female case 51 years old). Variant was absent in healthy controls. No segregation evidence. Supportive functional evidence.
More evidence including segregation information, genotype-phenotype correlation between DCM and/or congenital heart disease and ascertainment from diverse ancestries required.
Sources: LiteratureCreated: 25 Nov 2025, 3:23 p.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
Congenital heart disease MONDO:0005453 - KLF13-related; Dilated cardiomyopathy - MONDO:0005021, KLF13-related
Publications for gene: KLF13 were set to
Gene: klf13 has been classified as Amber List (Moderate Evidence).
Gene: klf13 has been classified as Amber List (Moderate Evidence).
gene: KLF13 was added gene: KLF13 was added to Mendeliome. Sources: Literature Mode of inheritance for gene: KLF13 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Phenotypes for gene: KLF13 were set to Congenital heart disease MONDO:0005453 - KLF13-related; Dilated cardiomyopathy - MONDO:0005021, KLF13-related Review for gene: KLF13 was set to AMBER
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at panelapp@genomicsengland.co.uk
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.