STAP1 p.Lys162=
c.486G>A · rs769900958 · VCV1743698
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0147%, 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 2.4 | GERP 0.98, phastCons 1 |
| Overall | ||
| CADD | 4.678 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0147%
African / African-American · 11/74,900 alleles
Filtering AF
0.00816%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00633%
Overall
0.000744%
12/1,613,590 alleles · ultra-rare
exomes 4/1,461,444 · genomes 8/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0147% | 6,809 |
| Admixed American | 0.00167% | 59,958 |
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
- STAP1
- Protein
- p.Lys162=
- Coding
- c.486G>A
- MANE Select
- NM_012108
- dbSNP
- rs769900958
- Type
- single nucleotide variant
- Location
- chr4:67581427 (GRCh38)
- Structure
- AlphaFold pLDDT 88.06
Similar variants
- STAP1 p.Lys162Glu Uncertain significance ★ ⚠ same residue
- STAP1 p.Gln192Arg Uncertain significance ★★ ⚠ same type
- STAP1 p.Leu288Val Uncertain significance ★★ ⚠ same type
- STAP1 c.120+6T>C Benign/Likely benign ★★ same type
- STAP1 c.192+102T>C Likely benign ★★ same type
- STAP1 c.192+10T>C Benign ★★ same type
- STAP1 c.530+11A>G Benign ★★ same type
- STAP1 c.530+60A>G 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/stap1-p-lys162 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown