RSPH3 p.Pro102=
c.306T>C · rs1583713398 · VCV752818
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 6.2e-05%)
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 -12 | GERP -9.7 |
| Overall | ||
| CADD | 0.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.2e-05%
Overall
6.2e-05%
1/1,614,126 alleles · very rare
exomes 1/1,461,820 · genomes 0/152,306 · 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.Pro102=
- Coding
- c.306T>C
- MANE Select
- NM_031924
- dbSNP
- rs1583713398
- Type
- single nucleotide variant
- Location
- chr6:158986320 (GRCh38)
- Gene constraint
- LOEUF 0.784 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 65.67 · 1 PDB
Similar variants
- 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
- RSPH3 c.-185G>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-pro102 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown