SP110 p.Ser573=
c.1719T>C · VCV4719518
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
hepatic veno-occlusive disease-immunodeficiency syndrome
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 -1.8 | GERP -3.9 |
| Overall | ||
| CADD | 0.67 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SP110
- Protein
- p.Ser573=
- Coding
- c.1719T>C
- MANE Select
- NM_080424
- Type
- single nucleotide variant
- Location
- chr2:230172162 (GRCh38)
- Gene constraint
- LOEUF 0.826 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 58.63
Disease context
hepatic veno-occlusive disease-immunodeficiency syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Hepatic veno-occlusive disease-immunodeficiency syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy
Similar variants
- SP110 c.1888-2A>G Likely pathogenic ★★ same condition
- SP110 p.Arg344Ter Pathogenic/Likely pathogenic ★★ same condition
- SP110 p.Arg421Ter Pathogenic/Likely pathogenic ★★ same condition
- SP110 p.Arg448Ter Pathogenic/Likely pathogenic ★★ same condition
- SP110 p.Arg554Ter Pathogenic/Likely pathogenic ★★ same condition
- SP110 p.Arg631Ter Pathogenic/Likely pathogenic ★★ same condition
- SP110 c.1591-6T>G Uncertain significance ★★ same condition
- SP110 c.583+3G>A 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/sp110-p-ser573 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown