GRPR p.Phe301=
c.903T>C · rs138384902 · VCV2660062
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0332%, afr)
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 -1.1 | GERP -3.9 |
| Overall | ||
| CADD | 7.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0332%
African / African-American · 19/57,162 alleles
Filtering AF
0.0217%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0181%
Overall
0.00207%
25/1,209,707 alleles · ultra-rare
exomes 13/1,097,767 · genomes 12/111,940 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0332% | 3,009 |
| Admixed American | 0.00655% | 15,270 |
| Remaining individualsnot grpmax-eligible | 0.0063% | 15,866 |
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
- GRPR
- Protein
- p.Phe301=
- Coding
- c.903T>C
- MANE Select
- NM_005314
- dbSNP
- rs138384902
- Type
- single nucleotide variant
- Location
- chrX:16152393 (GRCh38)
- Structure
- AlphaFold pLDDT 78.78 · 4 PDB
- Residue 301
- an α-helix
Similar variants
- GRPR p.Lys362= Likely benign ★★ same type
- GRPR p.Thr132= Benign ★★ same type
- GRPR p.Val220Ile Likely benign ★★ same type
- GRPR p.Ala136Val Uncertain significance ★ ⚠ same type
- GRPR p.Ala369Val Uncertain significance ★ ⚠ same type
- GRPR p.Arg144Trp Uncertain significance ★ ⚠ same type
- GRPR p.Arg261Gln Uncertain significance ★ ⚠ same type
- GRPR p.Arg287Leu 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/grpr-p-phe301 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown