GHSR p.Val153=
c.459G>C · VCV3629691
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 | <0.2 | all four deltas below 0.2 · C>T here scores Δ0.40 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.28 | GERP 0.026, phastCons 0.98 |
| Overall | ||
| CADD | 10.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00329%
South Asian · 3/91,082 alleles
Filtering AF
0.000875%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000186%
3/1,613,712 alleles · very rare
exomes 3/1,461,366 · genomes 0/152,346 · joint denominator
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
- GHSR
- Protein
- p.Val153=
- Coding
- c.459G>C
- MANE Select
- NM_198407
- Type
- single nucleotide variant
- Location
- chr3:172447955 (GRCh38)
- Gene constraint
- LOEUF 1.033 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.75 · 10 PDB
- Residue 153
- an α-helix
Similar variants
- GHSR p.Arg141Leu Uncertain significance ★★ ⚠ same type
- GHSR p.Arg141Pro Uncertain significance ★★ ⚠ same type
- GHSR p.Arg206Pro Uncertain significance ★★ ⚠ same type
- GHSR p.Arg237Trp Uncertain significance ★★ ⚠ same type
- GHSR p.Arg283Ter Uncertain significance ★★ same type
- GHSR p.Glu73Asp Uncertain significance ★★ ⚠ same type
- GHSR p.Glu9Lys Uncertain significance ★★ ⚠ same type
- GHSR p.Ile167Phe 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/ghsr-p-val153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown