GP1BA p.Phe207Ser
c.620T>C · VCV3339412
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
AlphaMissense
likely pathogenic
0.9461 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/2 damaging
AlphaMissense, SaProt · REVEL indeterminate
Conditions
1
GP1BA-related disorders
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9461 | likely pathogenic · top 4% in GP1BA |
|---|---|---|
| REVEL | 0.467 | indeterminate |
| SaProt | LLR -11.23 | damaging |
| ⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 0.89 | unconstrained · MANE · 1,223 bp · p 0.011 · regional, not allelic |
| Overall | ||
| CADD | 25.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GP1BA
- Protein
- p.Phe207Ser
- Coding
- c.620T>C
- MANE Select
- NM_000173
- Type
- single nucleotide variant
- Location
- chr17:4933224 (GRCh38)
- Gene constraint
- LOEUF 1.289 · pLI 0.10 (gnomAD)
- Structure
- AlphaFold pLDDT 64.65 · 22 PDB
- Residue 207
- a turn
Disease context
GP1BA-related disorders
Similar variants
- GP1BA p.Phe207Cys Uncertain significance ★ ⚠ same residue
- GP1BA p.Phe207= Likely benign ★ same residue
- GP1BA p.Ala172Val Pathogenic ★★ ⚠ same condition
- GP1BA p.Gly249Val Pathogenic/Likely pathogenic ★★ same condition
- GP1BA p.Leu83Phe Likely pathogenic ★★ ⚠ same condition
- GP1BA p.Met255Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
- GP1BA p.Val31Glu Uncertain significance ★★ ⚠ same condition
- GP1BA p.Asn198Ser Likely pathogenic ★ same condition
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/gp1ba-p-phe207ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown