GENE REFERENCE / HGNC:1494

ALX1

ALX homeobox 1

protein-coding gene12q21.31Gene information

What does this gene do?

The ALX1 gene provides instructions for making a protein that is a member of the homeobox protein family. Homeobox proteins direct the formation of body structures during early embryonic development. The ALX1 protein is necessary for normal development of the head and face, particularly the formation of the eyes, nose, and mouth, which begins around the fourth week of development. The ALX1 protein is a transcription factor, which means that it attaches (binds) to DNA and controls the activity of certain genes. Specifically, the protein controls the activity of genes that regulate cell growth and division (proliferation) and movement (migration), ensuring that cells grow and stop growing at specific times and that they are positioned correctly during development.

Source: MedlinePlus, National Library of Medicine. Source publication: 2025-09-26. Source review: 2014-04.

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
frontonasal dysplasia - severe microphthalmia - severe facial clefting syndromeMONDO:0013271 · Evaluated 2022-10-13	Autosomal recessive	DefinitiveCraniofacial Malformations 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: 89
Submissions for variants in or overlapping this gene: 119
Submissions explicitly reporting this gene: 99
Alleles reported pathogenic / likely pathogenic: 3
VariationIDs with uncertain significance: 47
VariationIDs with conflicting classifications: 1

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 ALX1?

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 3 alleles in ALX1 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 ALX1.

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

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