ARHGAP20

Chr 11

Rho GTPase activating protein 20

Also known as: RARHOGAP

NCBI Gene: 57569 ENSG00000137727 UniProt: Q9P2F6

The protein encoded by this gene is an activator of RHO-type GTPases, transducing a signal from RAP1 to RHO and impacting neurite outgrowth. [provided by RefSeq, Sep 2016]

Research

The protein encoded by this gene is an activator of RHO-type GTPases, transducing a signal from RAP1 to RHO and impacting neurite outgrowth. [provided by RefSeq, Sep 2016]

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.43

LOEUF

—

Mechanism

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.43LOEUF

pLI 0.029

Z-score 4.57

OE 0.27 (0.17–0.43)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.14Z-score

OE missense 0.87 (0.81–0.94)

533 obs / 612.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.27 (0.17–0.43)

0≤0.351.4

Missense OE?0.87 (0.81–0.94)

0≤0.61.4

Synonymous OE?1.01

0≤1.21.6

LoF obs/exp: 12 / 45.1Missense obs/exp: 533 / 612.4Syn Z: -0.10

Background carrier burden — how many people carry a rare variant somewhere in ARHGAP20?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 51

1,452 rare PASS variants

Rare truncating (LoF)

1 in 1,400

174 rare PASS variants

Rare synonymous (reference)

1 in 83

583 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for ARHGAP20. 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 73	1 in 1,300
South Asian	~43k	1 in 41	1 in 1,500
Remaining (unassigned)	~30k	1 in 36	1 in 2,500
European (Finnish)	~27k	1 in 110	1 in 5,300
Admixed American	~22k	1 in 43	1 in 1,300
African / African American	~21k	1 in 35	1 in 2,100
East Asian	~20k	1 in 53	1 in 2,700
Ashkenazi Jewish	~13k	1 in 130	1 in 2,100
Middle Eastern	~2,884	1 in 53	≈ 1 in 2,900

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.

Exome coverage (gnomAD): 12 of 15 coding exons well covered in gnomAD exomes; exons 1, 7, 12 marginal. Genomes: all 15.? see exons ↓