GP6 p.Pro39=
c.117C>A · VCV3617838
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
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 -0.62 | GERP -4.3 |
| Overall | ||
| CADD | 5.848 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/60,010 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.0018%
29/1,613,850 alleles · very rare
exomes 22/1,461,618 · genomes 7/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 12,002 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,619 |
| Finnishnot grpmax-eligible | 0.00313% | 31,954 |
| European (non-Finnish) | 0.00153% | 65,554 |
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
- GP6
- Protein
- p.Pro39=
- Coding
- c.117C>A
- MANE Select
- NM_016363
- Type
- single nucleotide variant
- Location
- chr19:55032347 (GRCh38)
- Gene constraint
- LOEUF 1.734 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 76.52 · 6 PDB
- Residue 39
- a β-strand; the ig-like c2-type 1 domain
Similar variants
- GP6 p.Trp160Ter Pathogenic ★★ same type
- GP6 c.*106A>C Uncertain significance ★★ same type
- GP6 c.*189C>T Uncertain significance ★★ same type
- GP6 c.*304C>T Uncertain significance ★★ same type
- GP6 c.*523G>C Uncertain significance ★★ same type
- GP6 c.*531T>C Uncertain significance ★★ same type
- GP6 c.*820T>C Uncertain significance ★★ same type
- GP6 p.Arg262Cys 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/gp6-p-pro39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown