ASCC3 p.Phe1287=
c.3861T>C · VCV4821409
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.49%, 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 0.53 | GERP -2.8, phastCons 0.77 |
| Overall | ||
| CADD | 3.857 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.49%
African / African-American · 368/75,038 alleles
Filtering AF
0.449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.433%
Overall
0.0263%
425/1,613,968 alleles · rare
exomes 227/1,461,680 · genomes 198/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.49% | 204 |
| Remaining individualsnot grpmax-eligible | 0.0496% | 2,016 |
| Middle Eastern | 0.0495% | 2,019 |
| Admixed American | 0.0233% | 4,287 |
| South Asian | 0.00659% | 15,180 |
| European (non-Finnish) | 0.000254% | 393,301 |
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
- ASCC3
- Protein
- p.Phe1287=
- Coding
- c.3861T>C
- MANE Select
- NM_006828
- Type
- single nucleotide variant
- Location
- chr6:100642621 (GRCh38)
- Gene constraint
- LOEUF 0.677 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.93 · 2 PDB
- Residue 1287
- a UniProt-annotated variant site (in mrt81; uncertain significance); the sec63 1 domain
Similar variants
- ASCC3 c.1597-2A>G Likely pathogenic ★★ same type
- ASCC3 c.1596+1G>T Uncertain significance ★★ same type
- ASCC3 p.Ala1186Val Uncertain significance ★★ ⚠ same type
- ASCC3 p.Ala94Val Uncertain significance ★★ ⚠ same type
- ASCC3 p.Arg1808His Uncertain significance ★★ ⚠ same type
- ASCC3 p.Arg1835Cys Uncertain significance ★★ ⚠ same type
- ASCC3 p.Arg630Cys Uncertain significance ★★ ⚠ same type
- ASCC3 p.Asn1607Ser 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/ascc3-p-phe1287 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown