GORAB p.Arg240His
c.719G>A · rs149924639 · VCV293661
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.258%, eas)
Conditions
1
geroderma osteodysplasticum
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.166 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 8.7 | GERP 2, phastCons 1 |
| Regional constraint | o/e 1.01 | unconstrained · MANE · 20 kb · p 0.84 · regional, not allelic |
| Overall | ||
| CADD | 23.8 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.258%
East Asian · 116/44,876 alleles
Filtering AF
0.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.206%
Overall
0.0159%
256/1,613,972 alleles · rare
exomes 240/1,461,730 · genomes 16/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.258% | 387 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| European (non-Finnish) | 0.0105% | 9,516 |
| Admixed American | 0.00667% | 15,002 |
| South Asian | 0.00329% | 30,355 |
| African / African-American | 0.00133% | 75,006 |
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
- GORAB
- Protein
- p.Arg240His
- Coding
- c.719G>A
- MANE Select
- NM_152281
- dbSNP
- rs149924639
- Type
- single nucleotide variant
- Location
- chr1:170552071 (GRCh38)
- Gene constraint
- LOEUF 0.802 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 71.86
- Residue 240
- the 'necessary for interaction with rchy1' region
Similar variants
- GORAB p.Arg240Cys Uncertain significance ★ same residue
- GORAB p.Arg240= Likely benign ★ same residue
- GORAB p.Arg262Ter Pathogenic/Likely pathogenic ★★ same condition
- GORAB p.Arg35Ter Pathogenic ★★ same condition
- GORAB p.Arg40Ter Pathogenic/Likely pathogenic ★★ same condition
- GORAB p.Gln64Ter Pathogenic ★★ same condition
- GORAB c.-21G>A Uncertain significance ★★ same condition
- GORAB c.-28C>G Uncertain significance ★★ same condition
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/gorab-p-arg240his (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown