EXOC4 p.Pro20=
c.60C>T · rs73436933 · VCV781114
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.79%, 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 0.32 | GERP -4.3, phastCons 0.99 |
| Overall | ||
| CADD | 12.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.79%
African / African-American · 2,842/75,050 alleles
Filtering AF
3.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.62%
Overall
0.19%
3,065/1,614,170 alleles · low-frequency
exomes 1,494/1,461,852 · genomes 1,571/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.79% | 26 |
| Remaining individualsnot grpmax-eligible | 0.158% | 631 |
| Admixed American | 0.147% | 682 |
| Middle Eastern | 0.099% | 1,010 |
| South Asian | 0.00549% | 18,218 |
| European (non-Finnish) | 0.00212% | 47,200 |
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
- EXOC4
- Protein
- p.Pro20=
- Coding
- c.60C>T
- MANE Select
- NM_021807
- dbSNP
- rs73436933
- Type
- single nucleotide variant
- Location
- chr7:133253161 (GRCh38)
- Gene constraint
- LOEUF 0.745 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.22 · 1 PDB
Similar variants
- EXOC4 p.Gly550Arg Benign ★★ ⚠ same type
- EXOC4 p.Ile926= Benign ★★ same type
- EXOC4 p.Leu749= Benign ★★ same type
- EXOC4 c.1417+54940G>A Uncertain significance ★ same type
- EXOC4 p.Ala153Val Uncertain significance ★ ⚠ same type
- EXOC4 p.Ala225Asp Uncertain significance ★ ⚠ same type
- EXOC4 p.Ala250Thr Uncertain significance ★ ⚠ same type
- EXOC4 p.Ala287Val 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/exoc4-p-pro20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown