RTN3 p.Val59=
c.177A>C · rs75523067 · VCV718662
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.16%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8.1 | GERP 2.3, phastCons 1 |
| Overall | ||
| CADD | 10.05 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.16%
East Asian · 970/44,840 alleles
Filtering AF
2.05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2%
Overall
0.08%
1,290/1,612,224 alleles · low-frequency
exomes 1,126/1,460,014 · genomes 164/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.16% | 46 |
| South Asian | 0.204% | 489 |
| Remaining individualsnot grpmax-eligible | 0.131% | 762 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.0117% | 8,573 |
| European (non-Finnish) | 0.00356% | 28,061 |
| African / African-American | 0.00267% | 37,495 |
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
- RTN3
- Protein
- p.Val59=
- Coding
- c.177A>C
- MANE Select
- NM_001265589
- dbSNP
- rs75523067
- Type
- single nucleotide variant
- Location
- chr11:63704885 (GRCh38)
- Gene constraint
- LOEUF 0.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 43.42 · 1 PDB
- Residue 59
- the 'disordered' region
Similar variants
- RTN3 p.Ser10= Benign ★★ same type
- RTN3 p.Ala198Thr Uncertain significance ★ ⚠ same type
- RTN3 p.Ala256Thr Uncertain significance ★ ⚠ same type
- RTN3 p.Ala2Val Uncertain significance ★ ⚠ same type
- RTN3 p.Ala321Val Uncertain significance ★ ⚠ same type
- RTN3 p.Ala448Gly Uncertain significance ★ ⚠ same type
- RTN3 p.Ala510Pro Uncertain significance ★ ⚠ same type
- RTN3 p.Ala657Val 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/rtn3-p-val59 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown