ARHGAP11A

Chr 15

Rho GTPase activating protein 11A

Also known as: GAP (1-12)

NCBI Gene: 9824 ENSG00000198826 UniProt: Q6P4F7 OMIM: 610589

This gene encodes a member of the Rho GTPase activating protein family. In response to DNA damage, the encoded protein interacts with the p53 tumor suppressor protein and stimulates its tetramerization, which results in cell-cycle arrest and apoptosis. A chromosomal deletion that includes this gene is one cause of Prader-Willi syndrome, and an intronic variant of this gene may be associated with sleep duration in children. This gene is highly expressed in colon cancers and in a human basal-like breast cancer cell line. This gene also produces a ARHGAP11A-SCG5 readthrough transcript and ARHGAP11A-SCG5 protein. [provided by RefSeq, Feb 2019]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.74

LOEUF

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.74LOEUF

pLI 0.000

Z-score 2.87

OE 0.52 (0.36–0.74)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.01Z-score

OE missense 1.00 (0.93–1.07)

522 obs / 522.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.52 (0.36–0.74)

0≤0.351.4

Missense OE?1.00 (0.93–1.07)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 21 / 40.7Missense obs/exp: 522 / 522.4Syn Z: 0.27

Background carrier burden — how many people carry a rare variant somewhere in ARHGAP11A?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 57

1,157 rare PASS variants

Rare truncating (LoF)

1 in 570

157 rare PASS variants

Rare synonymous (reference)

1 in 130

392 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ARHGAP11A. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 82	1 in 580
South Asian	~43k	1 in 61	1 in 470
Remaining (unassigned)	~30k	1 in 47	1 in 750
European (Finnish)	~27k	1 in 170	≈ 1 in 8,900
Admixed American	~22k	1 in 47	1 in 650
African / African American	~21k	1 in 40	1 in 640
East Asian	~20k	1 in 54	1 in 500
Ashkenazi Jewish	~13k	1 in 190	≈ 1 in 3,200
Middle Eastern	~2,884	1 in 50	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.