VPS13C p.Arg2004=
c.6010A>C · rs750062884 · VCV2645401
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 8.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,082 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000434%
7/1,613,840 alleles · very rare
exomes 6/1,461,652 · genomes 1/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,082 |
| European (non-Finnish) | 0.000509% | 196,647 |
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
- VPS13C
- Protein
- p.Arg2004=
- Coding
- c.6010A>C
- MANE Select
- NM_020821
- dbSNP
- rs750062884
- Type
- single nucleotide variant
- Location
- chr15:61931118 (GRCh38)
- Gene constraint
- LOEUF 0.857 · pLI <0.01 (gnomAD)
Similar variants
- VPS13C c.5868+1G>A Likely pathogenic ★★ same type
- VPS13C p.Arg2936Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13C p.Arg3652Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13C p.Arg371Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13C p.Arg567Ter Pathogenic/Likely pathogenic ★★ same type
- VPS13C p.Gln3257Ter Pathogenic ★★ same type
- VPS13C p.Glu3354Ter Pathogenic ★★ same type
- VPS13C p.Glu3407Ter Pathogenic/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/vps13c-p-arg2004 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown