GHR p.Phe85=
c.255C>T · rs2530643666 · VCV2754409
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.6 | GERP 0.89, phastCons 1 |
| Overall | ||
| CADD | 5.452 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,179,604 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,613,710 alleles · very rare
exomes 2/1,461,382 · genomes 0/152,328 · 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
- GHR
- Protein
- p.Phe85=
- Coding
- c.255C>T
- MANE Select
- NM_000163
- dbSNP
- rs2530643666
- Type
- single nucleotide variant
- Location
- chr5:42689008 (GRCh38)
- Gene constraint
- LOEUF 0.65 · pLI 0.16 (gnomAD)
- Structure
- AlphaFold pLDDT 59.70 · 11 PDB
- Residue 85
- a β-strand
Similar variants
- GHR c.266+83G>T Pathogenic/Likely pathogenic ★★ same type
- GHR c.267-2A>G Pathogenic/Likely pathogenic ★★ same type
- GHR c.440-1G>A Pathogenic/Likely pathogenic ★★ same type
- GHR c.618+792A>G Pathogenic/Likely pathogenic ★★ same type
- GHR p.Arg235Ter Pathogenic ★★ same type
- GHR p.Arg61Ter Pathogenic ★★ same type
- GHR p.Asn115Thr Pathogenic/Likely pathogenic ★★ same type
- GHR p.Asp170His Pathogenic/Likely 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/ghr-p-phe85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown