RALA p.Ile78=
c.234T>C · rs2534039047 · VCV2023445
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000678%, nfe)
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 -1.9 | GERP -4.4 |
| Overall | ||
| CADD | 6.347 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000678%
European (non-Finnish) · 8/1,179,890 alleles
Filtering AF
0.000292%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000211%
Overall
0.000496%
8/1,613,994 alleles · very rare
exomes 8/1,461,720 · genomes 0/152,274 · 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.Ile78=
- Coding
- c.234T>C
- MANE Select
- NM_005402
- dbSNP
- rs2534039047
- Type
- single nucleotide variant
- Location
- chr7:39690501 (GRCh38)
- Gene constraint
- LOEUF 0.54 · pLI 0.95 (gnomAD)
- Structure
- AlphaFold pLDDT 89.54 · 17 PDB
- Residue 78
- 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-ile78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown