SMC2

Chr 9AR

structural maintenance of chromosomes 2

Also known as: CAP-E, CAPE, SMC-2, SMC2L1

The protein is a central component of the condensin complex that converts interphase chromatin into condensed mitotic chromosomes by introducing positive supercoils into DNA. Mutations cause Smith-McCort dysplasia 2, a skeletal dysplasia with autosomal recessive inheritance. This gene is highly constrained against loss-of-function variants in the general population.

OMIMResearchSummary from RefSeq, OMIM, UniProt
ARLOEUF 0.231 OMIM phenotype
Clinical SummarySMC2
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.23LOEUF
pLI 1.000
Z-score 6.32
OE 0.13 (0.070.23)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
1.06Z-score
OE missense 0.88 (0.810.94)
517 obs / 589.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.13 (0.070.23)
00.351.4
Missense OE0.88 (0.810.94)
00.61.4
Synonymous OE1.04
01.21.6
LoF obs/exp: 8 / 61.4Missense obs/exp: 517 / 589.3Syn Z: -0.49

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

SMC2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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