OR1J2

Chr 9

olfactory receptor family 1 subfamily J member 2

Also known as: HG152, HSA5, OR1J3, OR1J5, OR9-19, OST044

NCBI Gene: 26740 ENSG00000197233 UniProt: Q8NGS2

The OR1J2 protein is an olfactory receptor that binds odorant molecules and initiates G protein-mediated signal transduction to trigger smell perception. No established disease associations have been reported for OR1J2 mutations. The predicted gain-of-function mechanism and high loss-of-function tolerance (pLI=0.09, LOEUF=1.89) suggest this gene is not highly constrained against variation.

ResearchSummary from RefSeq, UniProt, Mechanism

MultiplemechanismLOEUF 1.89

Clinical Summary— OR1J2

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Population Constraint (gnomAD)

Low constraint (pLI 0.09) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

28 unique Pathogenic / Likely Pathogenic· 246 VUS of 294 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint

1.89LOEUF

pLI 0.093

Z-score 0.04

OE 0.96 (0.26–1.89)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint

-0.41Z-score

OE missense 1.09 (0.96–1.23)

185 obs / 170.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios

LoF OE0.96 (0.26–1.89)

0≤0.351.4

Missense OE1.09 (0.96–1.23)

0≤0.61.4

Synonymous OE1.03

0≤1.21.6

LoF obs/exp: 1 / 1.0Missense obs/exp: 185 / 170.1Syn Z: -0.18

0.86top 5%

GOF

0.88top 5%

LOF

0.1399th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median

DNprediction 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.