GP9 p.Ala159=
c.477G>T · rs780042360 · VCV1562772
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000864%, nfe)
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 -2.1 | GERP -2.5 |
| Overall | ||
| CADD | 0.424 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000864%
European (non-Finnish) · 10/1,157,716 alleles
Filtering AF
0.000437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000318%
Overall
0.00064%
10/1,563,436 alleles · very rare
exomes 10/1,411,174 · genomes 0/152,262 · joint denominator
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
- GP9
- Protein
- p.Ala159=
- Coding
- c.477G>T
- MANE Select
- NM_000174
- dbSNP
- rs780042360
- Type
- single nucleotide variant
- Location
- chr3:129062216 (GRCh38)
- Structure
- AlphaFold pLDDT 84.43 · 2 PDB
- Residue 159
- an α-helix
Similar variants
- GP9 p.Ala159Thr Uncertain significance ★ ⚠ same residue
- GP9 p.Ala159fs Likely pathogenic ★★★ same residue
- GP9 p.Asn61Ser Pathogenic ★★★ same type
- GP9 p.Cys135Tyr Likely pathogenic ★★★ ⚠ same type
- GP9 p.Cys24Arg Likely pathogenic ★★★ same type
- GP9 p.Cys38Arg Likely pathogenic ★★★ same type
- GP9 p.Cys89Tyr Pathogenic ★★★ same type
- GP9 p.Leu56Pro 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/gp9-p-ala159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown