GRPR p.Lys362=
c.1086G>A · rs777024531 · VCV748394
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.688%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.006 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 5.408 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.688%
Middle Eastern · 30/4,362 alleles
Filtering AF
0.495%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.43%
Overall
0.0137%
165/1,205,117 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.688% | 145 |
| Remaining individualsnot grpmax-eligible | 0.0169% | 5,928 |
| Admixed American | 0.0153% | 6,541 |
| European (non-Finnish) | 0.0131% | 7,612 |
| African / African-American | 0.0035% | 28,533 |
| South Asian | 0.00176% | 56,722 |
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.Lys362=
- Coding
- c.1086G>A
- MANE Select
- NM_005314
- dbSNP
- rs777024531
- Type
- single nucleotide variant
- Location
- chrX:16152576 (GRCh38)
- Structure
- AlphaFold pLDDT 78.78 · 4 PDB
Similar variants
- 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
- GRPR p.Arg347Gln 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-lys362 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown