VPS13D p.Pro41=
c.123A>G · rs140004020 · VCV2063614
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.223%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -4.7 | GERP -2.9 |
| Overall | ||
| CADD | 1.341 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.223%
African / African-American · 167/75,056 alleles
Filtering AF
0.195%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.184%
Overall
0.0124%
200/1,614,178 alleles · rare
exomes 93/1,461,832 · genomes 107/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.223% | 449 |
| Admixed American | 0.0317% | 3,159 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,627 |
| South Asian | 0.0011% | 91,076 |
| European (non-Finnish) | 0.000678% | 147,503 |
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
- VPS13D
- Protein
- p.Pro41=
- Coding
- c.123A>G
- MANE Select
- NM_015378
- dbSNP
- rs140004020
- Type
- single nucleotide variant
- Location
- chr1:12242538 (GRCh38)
- Gene constraint
- LOEUF 0.426 · pLI 1.00 (gnomAD)
- Residue 41
- the chorein n-terminal domain
Similar variants
- VPS13D c.941+3A>G Pathogenic/Likely pathogenic ★★ same type
- VPS13D p.Ala4139Val Likely pathogenic ★★ ⚠ same type
- VPS13D p.Arg303Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13D p.Arg316Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13D p.Arg3253Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13D p.Arg3518Ter Likely pathogenic ★★ same type
- VPS13D p.Gly1190Asp Pathogenic/Likely pathogenic ★★ same type
- VPS13D p.Ala1265Ser 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/vps13d-p-pro41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown