LRATD2

Chr 8

LRAT domain containing 2

Also known as: BCMP101, FAM84B, NSE2

NCBI Gene: 157638 ENSG00000168672 UniProt: Q96KN1 OMIM: 609483

LRATD2 encodes a protein localized to the cytoplasm and plasma membrane, though its specific molecular function remains unclear. The gene shows very high constraint against loss-of-function variants (pLI = 0.0004), suggesting that biallelic mutations would likely cause severe developmental disorders, but no definitive disease associations have been established yet. This represents a candidate gene where pathogenic variants may cause as-yet-uncharacterized pediatric neurological or developmental phenotypes.

OMIM ResearchSummary from RefSeq

Located in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

GOFmechanismLOEUF 1.45

Clinical Summary— LRATD2

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.45LOEUF

pLI 0.000

Z-score 0.68

OE 0.74 (0.41–1.45)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.60Z-score

OE missense 0.88 (0.77–1.00)

165 obs / 188.0 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.74 (0.41–1.45)

0≤0.351.4

Missense OE?0.88 (0.77–1.00)

0≤0.61.4

Synonymous OE?1.03

0≤1.21.6

LoF obs/exp: 6 / 8.1Missense obs/exp: 165 / 188.0Syn Z: -0.19

This gene — mechanism propensity

0.5477th %ile

GOF

0.77top 25%

LOF

0.3163th %ile

The highest-scoring mechanism for this gene is gain-of-function.

GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.