GENE REFERENCE / HGNC:29079

KDM1A

lysine demethylase 1A

protein-coding gene1p36.12Basic gene details

What does this gene do?

The MedlinePlus data used here does not include an explanation of what this gene does. Its name and other identifying details come from HGNC.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
palatal anomalies-widely spaced teeth-facial dysmorphism-developmental delay syndromeMONDO:0014751 · Evaluated 2025-10-28	Autosomal dominant	DefinitiveSyndromic Disorders Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,262
Submissions for variants in or overlapping this gene: 1,644
Submissions explicitly reporting this gene: 1,613
Alleles reported pathogenic / likely pathogenic: 17
VariationIDs with uncertain significance: 671
VariationIDs with conflicting classifications: 21

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about KDM1A?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 17 alleles in KDM1A reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in KDM1A.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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