SEC23A p.Phe279=
c.837T>C · rs146187520 · VCV729892
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.139%, 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 0.55 | GERP -3.1, phastCons 0.93 |
| Overall | ||
| CADD | 7.225 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.139%
African / African-American · 104/74,980 alleles
Filtering AF
0.117%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.109%
Overall
0.00695%
112/1,611,210 alleles · rare
exomes 45/1,458,900 · genomes 67/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.139% | 721 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,603 |
| Admixed American | 0.00335% | 29,850 |
| European (non-Finnish) | 0.00017% | 589,074 |
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
- SEC23A
- Protein
- p.Phe279=
- Coding
- c.837T>C
- MANE Select
- NM_006364
- dbSNP
- rs146187520
- Type
- single nucleotide variant
- Location
- chr14:39076085 (GRCh38)
- Gene constraint
- LOEUF 0.708 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.86 · 38 PDB
Similar variants
- SEC23A p.Ala284Pro Uncertain significance ★★ ⚠ same type
- SEC23A p.Ala478Ser Uncertain significance ★★ ⚠ same type
- SEC23A p.Arg123Cys Uncertain significance ★★ ⚠ same type
- SEC23A p.Arg476His Uncertain significance ★★ ⚠ same type
- SEC23A p.Arg67His Uncertain significance ★★ ⚠ same type
- SEC23A p.Arg716Cys Uncertain significance ★★ ⚠ same type
- SEC23A p.Asn680Asp Uncertain significance ★★ ⚠ same type
- SEC23A p.Cys180Tyr 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/sec23a-p-phe279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown