RALGAPB p.Asp1284=
c.3852T>C · rs117581089 · VCV3039494
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.88%, eas)
Conditions
1
RALGAPB-related disorder
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 0.49 | GERP -3.4, phastCons 1 |
| Overall | ||
| CADD | 6.346 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.88%
East Asian · 845/44,862 alleles
Filtering AF
1.78%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.74%
Overall
0.106%
1,707/1,613,608 alleles · low-frequency
exomes 1,472/1,461,304 · genomes 235/152,304 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 1.88% | 53 |
| Admixed American | 0.86% | 116 |
| Remaining individualsnot grpmax-eligible | 0.141% | 710 |
| South Asian | 0.0813% | 1,230 |
| Finnishnot grpmax-eligible | 0.0625% | 1,600 |
| Middle Eastern | 0.0495% | 2,019 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0169% | 5,916 |
| European (non-Finnish) | 0.0109% | 9,216 |
| African / African-American | 0.0107% | 9,378 |
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
- RALGAPB
- Protein
- p.Asp1284=
- Coding
- c.3852T>C
- MANE Select
- NM_020336
- dbSNP
- rs117581089
- Type
- single nucleotide variant
- Location
- chr20:38567130 (GRCh38)
- Gene constraint
- LOEUF 0.202 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.28 · 1 PDB
- Residue 1284
- the rap-gap domain
Disease context
RALGAPB-related disorder
Similar variants
- RALGAPB p.Pro271Ala Uncertain significance ★ ⚠ same condition
- RALGAPB p.Val234= Uncertain significance ★ same condition
- RALGAPB p.Lys84Arg Uncertain significance ⚠ same condition
- RALGAPB c.554-10T>C Benign same condition
- RALGAPB p.Ala998= Benign same condition
- RALGAPB p.Asn276His Benign same condition
- RALGAPB p.Glu428= Benign same condition
- RALGAPB p.His1191Tyr Benign 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/ralgapb-p-asp1284 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown