CDC42EP1 p.His67=
c.201C>T · rs73418177 · VCV780654
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.98%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -14 | GERP -3.4 |
| Overall | ||
| CADD | 0.604 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.98%
African / African-American · 3,734/74,946 alleles
Filtering AF
4.85%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.79%
Overall
0.262%
4,220/1,608,742 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.98% | 20 |
| Remaining individualsnot grpmax-eligible | 0.352% | 284 |
| Middle Eastern | 0.298% | 336 |
| Admixed American | 0.26% | 385 |
| South Asian | 0.0209% | 4,775 |
| European (non-Finnish) | 0.00621% | 16,112 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0034% | 29,414 |
| East Asian | 0.00223% | 44,754 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDC42EP1
- Protein
- p.His67=
- Coding
- c.201C>T
- MANE Select
- NM_152243
- dbSNP
- rs73418177
- Type
- single nucleotide variant
- Location
- chr22:37566550 (GRCh38)
- Gene constraint
- LOEUF 1.863 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.46
Similar variants
- CDC42EP1 p.Leu344Pro Uncertain significance ★★ ⚠ same type
- CDC42EP1 p.Glu184= Benign ★★ same type
- CDC42EP1 p.Gly308= Benign ★★ same type
- CDC42EP1 p.Leu194= Benign ★★ same type
- CDC42EP1 p.Thr372= Benign ★★ same type
- CDC42EP1 p.Ala10Thr Uncertain significance ★ ⚠ same type
- CDC42EP1 p.Ala129Ser Uncertain significance ★ ⚠ same type
- CDC42EP1 p.Ala228Thr Uncertain significance ★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cdc42ep1-p-his67 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown