SEC61A1 p.Val162=
c.486C>T · rs754140750 · VCV3018597
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00924%, nfe)
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 -4.8, phastCons 0.1 |
| Overall | ||
| CADD | 8.327 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00924%
European (non-Finnish) · 109/1,180,006 alleles
Filtering AF
0.00782%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00727%
Overall
0.00694%
112/1,613,972 alleles · very rare
exomes 108/1,461,846 · genomes 4/152,126 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00924% | 10,826 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,240 |
| African / African-American | 0.00134% | 74,902 |
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
- SEC61A1
- Protein
- p.Val162=
- Coding
- c.486C>T
- MANE Select
- NM_013336
- dbSNP
- rs754140750
- Type
- single nucleotide variant
- Location
- chr3:128060531 (GRCh38)
- Gene constraint
- LOEUF 0.404 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 73.19 · 16 PDB
- Residue 162
- an α-helix
Similar variants
- SEC61A1 p.Leu89Phe Likely pathogenic ★★ same type
- SEC61A1 p.Ile100Thr Uncertain significance ★★ ⚠ same type
- SEC61A1 p.Ile161Thr Uncertain significance ★★ same type
- SEC61A1 p.Val192Ile Uncertain significance ★★ ⚠ same type
- SEC61A1 c.1168-4G>A Benign/Likely benign ★★ same type
- SEC61A1 c.220+128A>G Benign ★★ same type
- SEC61A1 c.220+129A>C Benign ★★ same type
- SEC61A1 c.221-53C>T Benign ★★ 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/sec61a1-p-val162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown