GRHPR p.Thr111=
c.333C>T · rs751686181 · VCV1160853
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00329%, 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 -12 | GERP -3.9 |
| Overall | ||
| CADD | 0.408 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,078 alleles
Filtering AF
0.00223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00198%
Overall
0.00266%
43/1,613,774 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00329% | 30,359 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| European (non-Finnish) | 0.00305% | 32,773 |
| Admixed American | 0.00167% | 59,994 |
| African / African-American | 0.00134% | 74,902 |
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
- GRHPR
- Protein
- p.Thr111=
- Coding
- c.333C>T
- MANE Select
- NM_012203
- dbSNP
- rs751686181
- Type
- single nucleotide variant
- Location
- chr9:37426583 (GRCh38)
- Gene constraint
- LOEUF 1.313 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 96.80 · 4 PDB
- Residue 111
- an α-helix
Similar variants
- GRHPR p.Thr111Ala Uncertain significance ★ ⚠ same residue
- GRHPR c.404+5G>A Likely pathogenic ★★ same type
- GRHPR c.493+2T>A Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.494-2A>G Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.734+1G>A Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.735-1G>A Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.83+1G>C Pathogenic/Likely pathogenic ★★ same type
- GRHPR c.84-2A>G 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/grhpr-p-thr111 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown