HSPD1 p.Pro161=
c.483T>C · rs758270645 · VCV515335
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.21e-05%)
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 0.2 | GERP -0.8, phastCons 0.19 |
| Overall | ||
| CADD | 8.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.21e-05%
Overall
6.21e-05%
1/1,610,110 alleles · very rare
exomes 1/1,457,834 · genomes 0/152,276 · 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
- HSPD1
- Protein
- p.Pro161=
- Coding
- c.483T>C
- MANE Select
- NM_002156
- dbSNP
- rs758270645
- Type
- single nucleotide variant
- Location
- chr2:197495321 (GRCh38)
- Gene constraint
- LOEUF 0.185 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.21 · 31 PDB
Similar variants
- HSPD1 p.Pro161Leu Uncertain significance ★ ⚠ same residue
- HSPD1 p.Val98Ile Pathogenic/Likely pathogenic ★★ ⚠ same type
- HSPD1 p.Ala476Ser Uncertain significance ★★ ⚠ same type
- HSPD1 p.Ala480Val Uncertain significance ★★ ⚠ same type
- HSPD1 p.Arg221Gln Uncertain significance ★★ ⚠ same type
- HSPD1 p.Arg37Gln Uncertain significance ★★ ⚠ same type
- HSPD1 p.Asn103Ser Uncertain significance ★★ ⚠ same type
- HSPD1 p.Asn208Thr 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/hspd1-p-pro161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown