SP110 p.Val392=
c.1176G>A · rs376997701 · VCV3050687
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
Conditions
1
SP110-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.13 | GERP 0.66 |
| Overall | ||
| CADD | 0.138 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,896 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.000929%
15/1,614,104 alleles · ultra-rare
exomes 10/1,461,856 · genomes 5/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,414 |
| African / African-American | 0.008% | 12,502 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| South Asian | 0.0011% | 91,078 |
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.Val392=
- Coding
- c.1176G>A
- MANE Select
- NM_080424
- dbSNP
- rs376997701
- Type
- single nucleotide variant
- Location
- chr2:230186097 (GRCh38)
- Gene constraint
- LOEUF 0.826 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.63
Disease context
SP110-related disorder
Similar variants
- SP110 p.Arg344Ter Pathogenic/Likely pathogenic ★★ same condition
- SP110 p.Gln231Ter Likely pathogenic ★ same condition
- SP110 p.Ser215fs Pathogenic ★★ same condition
- SP110 c.1888-2A>G 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
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-val392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown