Is LRBA p.Asp2810= (c.8430C>T) pathogenic?

LRBA p.Asp2810= (c.8430C>T) is classified Likely benign in LRBA (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-29). Ultra-rare (popmax 0.0134%, eas); Associated with Inborn genetic diseases.

What condition is associated with LRBA p.Asp2810= (c.8430C>T)?

LRBA p.Asp2810= (c.8430C>T) is associated with Inborn genetic diseases, combined immunodeficiency due to LRBA deficiency (ClinVar).

How common is LRBA p.Asp2810= (c.8430C>T) in the general population?

LRBA p.Asp2810= (c.8430C>T) is ultra-rare (popmax 0.0134%, eas) (gnomAD).

LRBA p.Asp2810=

c.8430C>T · rs766472618 · VCV1078919

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0134%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.073	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.8	GERP -3.5
Overall
CADD	0.216	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0134% East Asian · 6/44,878 alleles

Filtering AF 0.00969% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00905%

Overall 0.00985% 159/1,613,908 alleles · ultra-rare exomes 143/1,461,846 · genomes 16/152,062 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0134%	7,480
Admixed American	0.0133%	7,498
European (non-Finnish)	0.0113%	8,872
South Asian	0.00659%	15,180
African / African-American	0.00534%	18,720
Remaining individualsnot grpmax-eligible	0.0032%	31,237

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.Asp2810=
Coding: c.8430C>T
MANE Select: NM_001364905
dbSNP: rs766472618
Type: single nucleotide variant
Location: chr4:150277891 (GRCh38)
Gene constraint: LOEUF 0.515 · pLI <0.01 (gnomAD)

Full LRBA gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: combined immunodeficiency due to LRBA deficiency

Similar variants

LRBA p.Asp2810Glu Uncertain significance ★★ ⚠ same residue
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

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-asp2810 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown