RALA p.Val20=
c.60G>A · rs1168927459 · VCV1438238
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
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 2.6 | GERP -2.7, phastCons 1 |
| Overall | ||
| CADD | 9.162 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,180,000 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,098 alleles · very rare
exomes 2/1,461,848 · genomes 0/152,250 · 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
- RALA
- Protein
- p.Val20=
- Coding
- c.60G>A
- MANE Select
- NM_005402
- dbSNP
- rs1168927459
- Type
- single nucleotide variant
- Location
- chr7:39686727 (GRCh38)
- Gene constraint
- LOEUF 0.54 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 89.54 · 17 PDB
- Residue 20
- a β-strand
Similar variants
- RALA p.Thr156Ile Likely pathogenic ★★ same type
- RALA p.Val25Met Pathogenic/Likely pathogenic ★★ same type
- RALA p.Ala196Thr Uncertain significance ★★ ⚠ same type
- RALA p.Arg161Ter Uncertain significance ★★ same type
- RALA p.Arg176Ter Uncertain significance ★★ same type
- RALA p.Asp37Asn Uncertain significance ★★ ⚠ same type
- RALA p.Phe101Ser Uncertain significance ★★ ⚠ same type
- RALA c.114+10A>T Benign/Likely 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/rala-p-val20 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown