SP110 p.Val64=
c.192G>T · rs200472692 · VCV756476
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000254%, 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 -0.21 | GERP -0.003, phastCons 0.33 |
| Overall | ||
| CADD | 6.171 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000254%
European (non-Finnish) · 3/1,179,806 alleles
Filtering AF
6.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000186%
3/1,613,894 alleles · very rare
exomes 3/1,461,622 · genomes 0/152,272 · 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
- SP110
- Protein
- p.Val64=
- Coding
- c.192G>T
- MANE Select
- NM_080424
- dbSNP
- rs200472692
- Type
- single nucleotide variant
- Location
- chr2:230215074 (GRCh38)
- Gene constraint
- LOEUF 0.826 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.63
- Residue 64
- the hsr domain
Similar variants
- SP110 c.1888-2A>G Likely pathogenic ★★ same type
- SP110 p.Arg344Ter Pathogenic/Likely pathogenic ★★ same type
- SP110 p.Arg421Ter Pathogenic/Likely pathogenic ★★ same type
- SP110 p.Arg448Ter Pathogenic/Likely pathogenic ★★ same type
- SP110 p.Arg554Ter Pathogenic/Likely pathogenic ★★ same type
- SP110 p.Arg631Ter Pathogenic/Likely pathogenic ★★ same type
- SP110 c.1591-6T>G Uncertain significance ★★ same type
- SP110 c.583+3G>A 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/sp110-p-val64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown