STAP1 p.Leu138=
c.414G>C · rs149803575 · VCV1198972
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.07%, sas)
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 1.2 | GERP -4.1, phastCons 1 |
| Overall | ||
| CADD | 2.355 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.07%
South Asian · 976/91,048 alleles
Filtering AF
1.02%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.994%
Overall
0.08%
1,292/1,614,014 alleles · low-frequency
exomes 1,214/1,461,726 · genomes 78/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.07% | 93 |
| Middle Eastern | 0.297% | 337 |
| Remaining individualsnot grpmax-eligible | 0.0896% | 1,116 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0405% | 2,467 |
| European (non-Finnish) | 0.0182% | 5,488 |
| Admixed American | 0.015% | 6,668 |
| African / African-American | 0.004% | 25,014 |
| Finnishnot grpmax-eligible | 0.00312% | 32,006 |
| East Asian | 0.00223% | 44,878 |
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.Leu138=
- Coding
- c.414G>C
- MANE Select
- NM_012108
- dbSNP
- rs149803575
- Type
- single nucleotide variant
- Location
- chr4:67581355 (GRCh38)
- Structure
- AlphaFold pLDDT 88.06
Similar variants
- 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
- STAP1 c.730-41G>C 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-leu138 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown