C9 p.Val426del
c.1273GTT[1] · rs2479164653 · VCV2001436
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3 | GERP 2.1, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,058 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000274%
4/1,460,224 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,353 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,446 |
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
- C9
- Protein
- p.Val426del
- Coding
- c.1273GTT[1]
- MANE Select
- NM_001737
- dbSNP
- rs2479164653
- Type
- Microsatellite
- Location
- chr5:39306755 (GRCh38)
- Gene constraint
- LOEUF 1.223 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 79.32 · 9 PDB
- Residue 426
- the macpf domain; a β-strand
Similar variants
- C9 p.Ser395fs Pathogenic/Likely pathogenic ★★ same type
- C9 p.Glu92fs Pathogenic ★ same type
- C9 p.Asp424del Uncertain significance ★ same type
- C9 p.Ile476_Tyr477del Uncertain significance ★ same type
- C9 p.Thr318del 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/c9-p-val426del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown