SPR p.Phe181=
c.543C>T · rs903787203 · VCV2893216
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00393%, nfe)
Conditions
1
dystonic disorder
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 1.3 | GERP -1, phastCons 0.77 |
| Overall | ||
| CADD | 13.51 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00393%
European (non-Finnish) · 46/1,170,798 alleles
Filtering AF
0.00301%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00269%
Overall
0.00288%
46/1,598,262 alleles · very rare
exomes 45/1,446,038 · genomes 1/152,224 · 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
- SPR
- Protein
- p.Phe181=
- Coding
- c.543C>T
- MANE Select
- NM_003124
- dbSNP
- rs903787203
- Type
- single nucleotide variant
- Location
- chr2:72888552 (GRCh38)
- Gene constraint
- LOEUF 1.528 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.71 · 14 PDB
- Residue 181
- a UniProt-annotated variant site (in drdsprd); an α-helix
Similar variants
- SPR p.Arg150Gly Pathogenic ★★ same condition
- SPR p.Arg219Ter Pathogenic ★★ same condition
- SPR p.Cys171Tyr Likely pathogenic ★★ same condition
- SPR p.Gln182Ter Pathogenic ★★ same condition
- SPR p.Gln239Ter Pathogenic ★★ same condition
- SPR p.Lys230Ter Pathogenic/Likely pathogenic ★★ same condition
- SPR p.Lys251Ter Pathogenic ★★ same condition
- SPR c.304+5G>C 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/spr-p-phe181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown