RALA p.Val114=
c.342A>G · rs1220259341 · VCV1669553
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00403%, 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 4.4 | GERP -0.37, phastCons 1 |
| Overall | ||
| CADD | 10.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00403%
African / African-American · 3/74,382 alleles
Filtering AF
0.00107%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000497%
Overall
0.000312%
5/1,603,616 alleles · very rare
exomes 3/1,451,400 · genomes 2/152,216 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00403% | 24,794 |
| East Asian | 0.00223% | 44,820 |
| South Asian | 0.00112% | 89,572 |
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.Val114=
- Coding
- c.342A>G
- MANE Select
- NM_005402
- dbSNP
- rs1220259341
- Type
- single nucleotide variant
- Location
- chr7:39696703 (GRCh38)
- Gene constraint
- LOEUF 0.54 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 89.54 · 17 PDB
- Residue 114
- an α-helix
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-val114 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown