LRBA p.Ala2302=
c.6906A>G · rs142336513 · VCV717286
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0894%, afr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.263 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5 | GERP -3.8 |
| Overall | ||
| CADD | 1.663 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0894%
African / African-American · 67/74,918 alleles
Filtering AF
0.0722%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.066%
Overall
0.00477%
77/1,612,768 alleles · ultra-rare
exomes 42/1,460,558 · genomes 35/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0894% | 1,118 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,606 |
| Admixed American | 0.00501% | 19,961 |
| South Asian | 0.0011% | 90,906 |
| European (non-Finnish) | 0.00017% | 589,616 |
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
- LRBA
- Protein
- p.Ala2302=
- Coding
- c.6906A>G
- MANE Select
- NM_001364905
- dbSNP
- rs142336513
- Type
- single nucleotide variant
- Location
- chr4:150436739 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI <0.01 (gnomAD)
- Residue 2302
- the beach domain; a β-strand
Similar variants
- LRBA c.216+1G>C Pathogenic/Likely pathogenic ★★ same condition
- LRBA c.2259-2A>G Likely pathogenic ★★ same condition
- LRBA c.2767-2A>G Likely pathogenic ★★ same condition
- LRBA c.4159-1G>T Likely pathogenic ★★ same condition
- LRBA c.5518+2T>C Likely pathogenic ★★ same condition
- LRBA c.5519-1G>A Likely pathogenic ★★ same condition
- LRBA c.5646-2A>T Pathogenic ★★ same condition
- LRBA p.Arg1445Ter Pathogenic ★★ 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/lrba-p-ala2302 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown