GP9 p.Pro105=
c.315C>T · rs755563532 · VCV1557959
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00549%, sas)
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 -11 | GERP -4.3 |
| Overall | ||
| CADD | 3.092 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00549%
South Asian · 5/91,066 alleles
Filtering AF
0.0021%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00136%
Overall
0.000558%
9/1,612,468 alleles · very rare
exomes 7/1,460,220 · genomes 2/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00549% | 18,213 |
| African / African-American | 0.00267% | 37,462 |
| European (non-Finnish) | 0.00017% | 589,769 |
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.Pro105=
- Coding
- c.315C>T
- MANE Select
- NM_000174
- dbSNP
- rs755563532
- Type
- single nucleotide variant
- Location
- chr3:129062054 (GRCh38)
- Structure
- AlphaFold pLDDT 84.43 · 2 PDB
- Residue 105
- an α-helix; the lrrct domain
Similar variants
- GP9 p.Pro105Ser Uncertain significance ★ ⚠ 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
- GP9 p.Leu7Pro 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-pro105 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown