GP9 p.Ser65=
c.195C>T · rs754789523 · VCV1638414
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
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 -7.2 | GERP -3.1 |
| Overall | ||
| CADD | 4.574 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00437%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00309%
Overall
0.00093%
15/1,613,760 alleles · ultra-rare
exomes 7/1,461,508 · genomes 8/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.00934% | 10,706 |
| Finnishnot grpmax-eligible | 0.00157% | 63,868 |
| European (non-Finnish) | 0.000509% | 196,650 |
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.Ser65=
- Coding
- c.195C>T
- MANE Select
- NM_000174
- dbSNP
- rs754789523
- Type
- single nucleotide variant
- Location
- chr3:129061934 (GRCh38)
- Structure
- AlphaFold pLDDT 84.43 · 2 PDB
Similar variants
- 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
- GP9 p.Leu7Pro Likely pathogenic ★★★ ⚠ same type
- GP9 p.Phe71Cys 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-ser65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown