EXOC3 p.Ser78=
c.234G>A · rs180921423 · VCV721259
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.997%, eas)
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 -4.7 | GERP -3.7 |
| Overall | ||
| CADD | 1.18 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.997%
East Asian · 429/43,014 alleles
Filtering AF
0.919%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.889%
Overall
0.0732%
1,159/1,584,356 alleles · rare
exomes 945/1,432,022 · genomes 214/152,334 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.997% | 100 |
| Remaining individualsnot grpmax-eligible | 0.592% | 169 |
| South Asian | 0.245% | 409 |
| Admixed American | 0.115% | 870 |
| African / African-American | 0.0781% | 1,281 |
| European (non-Finnish) | 0.00275% | 36,414 |
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
- EXOC3
- Protein
- p.Ser78=
- Coding
- c.234G>A
- MANE Select
- NM_007277
- dbSNP
- rs180921423
- Type
- single nucleotide variant
- Location
- chr5:447622 (GRCh38)
- Gene constraint
- LOEUF 0.475 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.79
Similar variants
- EXOC3 p.Pro303Arg Benign ★★ ⚠ same type
- EXOC3 p.Ser42= Benign ★★ same type
- EXOC3 p.Ala137Val Uncertain significance ★ ⚠ same type
- EXOC3 p.Ala318Ser Uncertain significance ★ ⚠ same type
- EXOC3 p.Ala333Thr Uncertain significance ★ ⚠ same type
- EXOC3 p.Ala37Val Uncertain significance ★ ⚠ same type
- EXOC3 p.Ala469Val Uncertain significance ★ ⚠ same type
- EXOC3 p.Ala533Thr 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/exoc3-p-ser78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown