RTN4IP1 p.Val24=
c.72T>A · rs769807848 · VCV1090319
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, afr)
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 1.5 | GERP -0.27 |
| Overall | ||
| CADD | 5.543 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,936 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000186%
3/1,614,034 alleles · very rare
exomes 2/1,461,818 · genomes 1/152,216 · 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
- RTN4IP1
- Protein
- p.Val24=
- Coding
- c.72T>A
- MANE Select
- NM_032730
- dbSNP
- rs769807848
- Type
- single nucleotide variant
- Location
- chr6:106628950 (GRCh38)
- Gene constraint
- LOEUF 0.952 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.54 · 1 PDB
Similar variants
- RTN4IP1 c.1083+2T>C Pathogenic/Likely pathogenic ★★ same type
- RTN4IP1 c.620+1G>C Likely pathogenic ★★ same type
- RTN4IP1 c.806+1G>A Pathogenic ★★ same type
- RTN4IP1 p.Arg103His Pathogenic ★★ same type
- RTN4IP1 p.Arg310Ter Pathogenic ★★ same type
- RTN4IP1 p.Lys201Ter Pathogenic ★★ same type
- RTN4IP1 p.Ser293Ter Pathogenic/Likely pathogenic ★★ same type
- RTN4IP1 p.Trp20Ter Pathogenic/Likely pathogenic ★★ 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/rtn4ip1-p-val24 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown