EXOC3 p.Ser42=
c.126C>T · rs115207857 · VCV778863
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.22%, 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 -13 | |
| Overall | ||
| CADD | 1.049 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.22%
African / African-American · 3,157/74,804 alleles
Filtering AF
4.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.05%
Overall
0.792%
12,737/1,608,386 alleles · low-frequency
exomes 10,423/1,456,106 · genomes 2,314/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.22% | 24 |
| Amishnot grpmax-eligible | 2.64% | 38 |
| South Asian | 1.33% | 75 |
| Remaining individualsnot grpmax-eligible | 0.689% | 145 |
| European (non-Finnish) | 0.64% | 156 |
| Middle Eastern | 0.622% | 161 |
| Admixed American | 0.47% | 213 |
| Finnishnot grpmax-eligible | 0.0863% | 1,159 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0548% | 1,823 |
| East Asian | 0.0134% | 7,474 |
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.Ser42=
- Coding
- c.126C>T
- MANE Select
- NM_007277
- dbSNP
- rs115207857
- Type
- single nucleotide variant
- Location
- chr5:446331 (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.Ser78= 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-ser42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown