CDC42SE1

Chr 1

CDC42 small effector 1

Also known as: SCIP1, SPEC1

NCBI Gene: 56882 ENSG00000197622 UniProt: Q9NRR8 OMIM: 619456

Predicted to enable GTPase inhibitor activity. Predicted to be involved in signal transduction. Located in cell junction. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

Predicted to enable GTPase inhibitor activity. Predicted to be involved in signal transduction. Located in cell junction. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.63

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.63LOEUF

pLI 0.004

Z-score 0.52

OE 0.76 (0.37–1.63)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

1.01Z-score

OE missense 0.59 (0.43–0.80)

28 obs / 47.7 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.76 (0.37–1.63)

0≤0.351.4

Missense OE?0.59 (0.43–0.80)

0≤0.61.4

Synonymous OE?0.80

0≤1.21.6

LoF obs/exp: 4 / 5.3Missense obs/exp: 28 / 47.7Syn Z: 0.60

Background carrier burden — how many people carry a rare variant somewhere in CDC42SE1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 1,200

86 rare PASS variants

Rare truncating (LoF)

1 in 6,900

20 rare PASS variants

Rare synonymous (reference)

1 in 2,400

27 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for CDC42SE1. 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 1,200	1 in 7,300
South Asian	~43k	1 in 510	≈ 1 in 14,000
Remaining (unassigned)	~30k	1 in 1,300	≈ 1 in 7,500
European (Finnish)	~27k	≈ 1 in 6,700	none seen
Admixed American	~22k	1 in 830	≈ 1 in 22,000
African / African American	~21k	1 in 850	≈ 1 in 8,400
East Asian	~20k	1 in 2,000	1 in 1,000
Ashkenazi Jewish	~13k	≈ 1 in 6,500	≈ 1 in 13,000
Middle Eastern	~2,884	≈ 1 in 580	none seen

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): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓