RSPH3 p.Ser411=
c.1233C>G · rs1777884482 · VCV3033091
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
Conditions
1
RSPH3-related 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 0.83 | GERP 2.4 |
| Overall | ||
| CADD | 0.997 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,612,242 alleles · very rare
exomes 0/1,460,136 · genomes 1/152,106 · 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
- RSPH3
- Protein
- p.Ser411=
- Coding
- c.1233C>G
- MANE Select
- NM_031924
- dbSNP
- rs1777884482
- Type
- single nucleotide variant
- Location
- chr6:158977562 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 65.67 · 1 PDB
Disease context
RSPH3-related disorder
Similar variants
- RSPH3 c.205-2A>G Pathogenic ★★ same condition
- RSPH3 p.Arg220Ter Likely pathogenic ★ same condition
- RSPH3 c.-292T>A Likely benign same condition
- RSPH3 c.-302_-301del Pathogenic/Likely pathogenic ★★ same condition
- RSPH3 c.-85dup Likely pathogenic same condition
- RSPH3 c.859+1G>T Pathogenic/Likely pathogenic ★★ same type
- RSPH3 c.-95G>A Pathogenic ★★ same type
- RSPH3 p.Gln94Ter 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/rsph3-p-ser411 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown