RNLS p.Gln53=
c.159G>A · rs142003651 · VCV1654256
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.394%, afr)
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 0.046 | GERP 0.67, phastCons 0.002 |
| Overall | ||
| CADD | 7.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.394%
African / African-American · 296/75,052 alleles
Filtering AF
0.357%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.343%
Overall
0.0234%
377/1,614,086 alleles · rare
exomes 233/1,461,740 · genomes 144/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.394% | 254 |
| Middle Eastern | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.04% | 2,500 |
| Admixed American | 0.0367% | 2,727 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,919 |
| European (non-Finnish) | 0.00195% | 51,304 |
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.Gln53=
- Coding
- c.159G>A
- MANE Select
- NM_001031709
- dbSNP
- rs142003651
- Type
- single nucleotide variant
- Location
- chr10:88582267 (GRCh38)
- Gene constraint
- LOEUF 1.206 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 96.79 · 1 PDB
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-gln53 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown