GENE REFERENCE / HGNC:11111

SMC1A

structural maintenance of chromosomes 1A

protein-coding geneXp11.22Gene information

What does this gene do?

The SMC1A gene provides instructions for making a protein that is part of the structural maintenance of chromosomes (SMC) family. Within the nucleus, SMC proteins help regulate the structure and organization of chromosomes.

The protein produced from the SMC1A gene helps control chromosomes during cell division. Before cells divide, they must copy all of their chromosomes. The copied DNA from each chromosome is arranged into two identical structures, called sister chromatids, which are attached to one another during the early stages of cell division. The SMC1A protein is part of a protein group called the cohesin complex that holds the sister chromatids together.

Researchers believe that the SMC1A protein, as a structural component of the cohesin complex, also plays important roles in stabilizing cells' genetic information, repairing damaged DNA, and regulating the activity of certain genes that are essential for normal development.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-05-02. Source review: 2022-04.

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
X-linked complex neurodevelopmental disorderMONDO:0100148 · Evaluated 2019-06-19	X-linked	DefinitiveIntellectual Disability and Autism 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: 1,427
Submissions for variants in or overlapping this gene: 1,961
Submissions explicitly reporting this gene: 1,760
Alleles reported pathogenic / likely pathogenic: 235
VariationIDs with uncertain significance: 413
VariationIDs with conflicting classifications: 57

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 SMC1A?

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 235 alleles in SMC1A 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 SMC1A.

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

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