HSPD1 p.Val201=
c.603A>G · rs146598485 · VCV219636
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.62%, eas)
Conditions
2
Spastic paraplegia
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 0.11 | GERP -2.1, phastCons 0.98 |
| Overall | ||
| CADD | 10.73 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.62%
East Asian · 1,168/44,634 alleles
Filtering AF
2.49%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.44%
Overall
0.0952%
1,503/1,578,598 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.62% | 38 |
| Remaining individualsnot grpmax-eligible | 0.227% | 441 |
| Middle Eastern | 0.0673% | 1,486 |
| South Asian | 0.0531% | 1,882 |
| African / African-American | 0.0363% | 2,753 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0102% | 9,795 |
| European (non-Finnish) | 0.00932% | 10,727 |
| Admixed American | 0.00833% | 11,998 |
| Finnishnot grpmax-eligible | 0.00312% | 32,017 |
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.Val201=
- Coding
- c.603A>G
- MANE Select
- NM_002156
- dbSNP
- rs146598485
- Type
- single nucleotide variant
- Location
- chr2:197494660 (GRCh38)
- Gene constraint
- LOEUF 0.185 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 88.21 · 31 PDB
- Residue 201
- a β-strand
Similar variants
- HSPD1 p.Val98Ile Pathogenic/Likely pathogenic ★★ ⚠ same condition
- HSPD1 p.Ala476Ser Uncertain significance ★★ ⚠ same condition
- HSPD1 p.Arg221Gln Uncertain significance ★★ ⚠ same condition
- HSPD1 p.Arg37Gln Uncertain significance ★★ ⚠ same condition
- HSPD1 p.Asn103Ser Uncertain significance ★★ ⚠ same condition
- HSPD1 p.Asn208Thr Uncertain significance ★★ ⚠ same condition
- HSPD1 p.Asp149His Uncertain significance ★★ ⚠ same condition
- HSPD1 p.Cys442Arg Uncertain significance ★★ ⚠ same condition
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-val201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown