VPS41 p.Val240=
c.720G>A · rs1001476 · VCV1250036
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 30.3%, afr) — too common for a highly-penetrant pathogenic allele
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 -0.08 | GERP -5, phastCons 0.82 |
| Overall | ||
| CADD | 6.239 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
30.3%
African / African-American · 22,708/74,880 alleles
Filtering AF
30%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 29.9%
Overall
7.41%
119,490/1,612,908 alleles · common
exomes 99,969/1,460,728 · genomes 19,521/152,180 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 30.3% | 3 |
| Middle Eastern | 8.99% | 11 |
| Remaining individualsnot grpmax-eligible | 7.57% | 13 |
| Finnishnot grpmax-eligible | 7.17% | 14 |
| Ashkenazi Jewishnot grpmax-eligible | 6.9% | 14 |
| European (non-Finnish) | 6.7% | 15 |
| Admixed American | 5.61% | 18 |
| Amishnot grpmax-eligible | 5.38% | 19 |
| South Asian | 2.69% | 37 |
| East Asian | 0.0178% | 5,608 |
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
- VPS41
- Protein
- p.Val240=
- Coding
- c.720G>A
- MANE Select
- NM_014396
- dbSNP
- rs1001476
- Type
- single nucleotide variant
- Location
- chr7:38789865 (GRCh38)
- Gene constraint
- LOEUF 0.904 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.63
- Residue 240
- the 'interaction with arl8b' region
Similar variants
- VPS41 c.61-1G>A Uncertain significance ★★ same type
- VPS41 p.Ala804Gly Uncertain significance ★★ ⚠ same type
- VPS41 p.Arg208Trp Uncertain significance ★★ ⚠ same type
- VPS41 p.Ile464Thr Uncertain significance ★★ ⚠ same type
- VPS41 p.Lys841Glu Uncertain significance ★★ ⚠ same type
- VPS41 p.Phe123Ser Uncertain significance ★★ ⚠ same type
- VPS41 p.Val539Ile Uncertain significance ★★ ⚠ same type
- VPS41 p.His813= Likely 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/vps41-p-val240 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown