RSPH3 p.Ala4=
c.12G>A · rs1239817454 · VCV791279
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,597,542)
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 0.34 | GERP -1.1 |
| Overall | ||
| CADD | 7.429 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,597,542). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- RSPH3
- Protein
- p.Ala4=
- Coding
- c.12G>A
- MANE Select
- NM_031924
- dbSNP
- rs1239817454
- Type
- single nucleotide variant
- Location
- chr6:158999539 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 65.67 · 1 PDB
Similar variants
- RSPH3 p.Ala4Thr Uncertain significance ★★ ⚠ same residue
- RSPH3 c.205-2A>G Pathogenic ★★ same type
- RSPH3 c.859+1G>T Pathogenic/Likely pathogenic ★★ same type
- RSPH3 c.-95G>A Pathogenic ★★ same type
- RSPH3 p.Gln94Ter Likely pathogenic ★★ same type
- RSPH3 c.859+5G>A Uncertain significance ★★ same type
- RSPH3 c.-10G>T Uncertain significance ★★ ⚠ same type
- RSPH3 c.-120C>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/rsph3-p-ala4 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown