VPS13A p.Pro2602=
c.7806G>A · rs745464654 · VCV2054570
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.69 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.65 | loss · gain 0.04 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 8.6 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 20.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,016 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000248%
4/1,613,428 alleles · very rare
exomes 4/1,461,240 · genomes 0/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,016 |
| South Asian | 0.0011% | 90,978 |
| European (non-Finnish) | 0.00017% | 589,908 |
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
- VPS13A
- Protein
- p.Pro2602=
- Coding
- c.7806G>A
- MANE Select
- NM_033305
- dbSNP
- rs745464654
- Type
- single nucleotide variant
- Location
- chr9:77356867 (GRCh38)
- Gene constraint
- LOEUF 0.696 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Residue 2602
- a UniProt-annotated variant site (in chac)
Similar variants
- VPS13A p.Pro2602Leu Uncertain significance ★★ ⚠ same residue
- VPS13A p.Pro2602Ala Uncertain significance ★ ⚠ same residue
- VPS13A c.144+1G>C Pathogenic ★★ same type
- VPS13A c.1596-1G>C Pathogenic/Likely pathogenic ★★ same type
- VPS13A c.1596-2A>G Pathogenic ★★ same type
- VPS13A c.188-2A>G Likely pathogenic ★★ same type
- VPS13A c.2037+1G>A Likely pathogenic ★★ same type
- VPS13A c.2427+1G>A Likely pathogenic ★★ 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/vps13a-p-pro2602 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown