RTN3 p.Asn337=
c.1011C>T · rs867805352 · VCV2641901
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.247%, mid)
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 -0.24 | GERP -2.6, phastCons 0.51 |
| Overall | ||
| CADD | 6.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.247%
Middle Eastern · 15/6,084 alleles
Filtering AF
0.152%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.123%
Overall
0.00192%
31/1,614,016 alleles · rare
exomes 29/1,461,880 · genomes 2/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.247% | 406 |
| South Asian | 0.00659% | 15,180 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,242 |
| African / African-American | 0.00267% | 37,449 |
| European (non-Finnish) | 0.000508% | 196,674 |
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.Asn337=
- Coding
- c.1011C>T
- MANE Select
- NM_001265589
- dbSNP
- rs867805352
- Type
- single nucleotide variant
- Location
- chr11:63719513 (GRCh38)
- Gene constraint
- LOEUF 0.712 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 43.42 · 1 PDB
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-asn337 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown