RNLS p.Ala313=
c.939A>T · rs756499748 · VCV668189
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.025%, amr)
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 -1.2 | GERP -2.9 |
| Overall | ||
| CADD | 7.676 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.025%
Admixed American · 15/59,906 alleles
Filtering AF
0.0154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0125%
Overall
0.00093%
15/1,613,294 alleles · ultra-rare
exomes 15/1,461,104 · genomes 0/152,190 · 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
- RNLS
- Protein
- p.Ala313=
- Coding
- c.939A>T
- MANE Select
- NM_001031709
- dbSNP
- rs756499748
- Type
- single nucleotide variant
- Location
- chr10:88285444 (GRCh38)
- Gene constraint
- LOEUF 1.206 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.79 · 1 PDB
- Residue 313
- a β-strand
Similar variants
- RNLS p.Asp102Glu Uncertain significance ★★ ⚠ same type
- RNLS p.His307Leu Uncertain significance ★★ ⚠ same type
- RNLS p.Ile226Thr Uncertain significance ★★ ⚠ same type
- RNLS p.Leu335Pro Uncertain significance ★★ ⚠ same type
- RNLS p.Pro249Leu Uncertain significance ★★ ⚠ same type
- RNLS p.Ser217Gly Uncertain significance ★★ ⚠ same type
- RNLS p.Thr160Pro Uncertain significance ★★ ⚠ same type
- RNLS c.224+115A>G Benign ★★ 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/rnls-p-ala313 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown