RTN4 p.Arg854=
c.2562A>G · rs1420520344 · VCV717142
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0227%, 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 1.9 | GERP 0.38, phastCons 1 |
| Overall | ||
| CADD | 7.787 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0227%
African / African-American · 17/74,910 alleles
Filtering AF
0.0144%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0119%
Overall
0.00105%
17/1,613,640 alleles · ultra-rare
exomes 5/1,461,458 · genomes 12/152,182 · 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
- RTN4
- Protein
- p.Arg854=
- Coding
- c.2562A>G
- MANE Select
- NM_020532
- dbSNP
- rs1420520344
- Type
- single nucleotide variant
- Location
- chr2:55025537 (GRCh38)
- Gene constraint
- LOEUF 0.546 · pLI 0.38 (gnomAD)
- Structure
- AlphaFold pLDDT 40.92 · 2 PDB
Similar variants
- RTN4 p.Glu899Gln Benign ★★ same type
- RTN4 p.Gly1070Ala Likely benign ★★ same type
- RTN4 p.Leu620= Benign ★★ same type
- RTN4 p.Leu814Met Likely benign ★★ same type
- RTN4 p.Pro992= Benign ★★ same type
- RTN4 p.Ser440Asn Benign ★★ same type
- RTN4 p.Ser920Cys Benign ★★ same type
- RTN4 p.Thr450Met 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/rtn4-p-arg854 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown