LRBA p.Phe2392=
c.7176T>C · rs368578594 · VCV1979713
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0174%, afr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.291 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 6.686 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0174%
African / African-American · 13/74,894 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00813%
Overall
0.00093%
15/1,613,378 alleles · ultra-rare
exomes 6/1,461,202 · genomes 9/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0174% | 5,761 |
| Admixed American | 0.00167% | 59,930 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,460 |
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.Phe2392=
- Coding
- c.7176T>C
- MANE Select
- NM_001364905
- dbSNP
- rs368578594
- Type
- single nucleotide variant
- Location
- chr4:150415456 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI <0.01 (gnomAD)
- Residue 2392
- the beach domain
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-phe2392 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown