OR13D1

Chr 9

olfactory receptor family 13 subfamily D member 1

Also known as: OR9-15

NCBI Gene: 286365 ENSG00000179055 UniProt: Q8NGV5

OR13D1 encodes an olfactory receptor that interacts with odorant molecules to initiate neuronal responses triggering smell perception through G-protein-coupled receptor signaling. No disease associations have been established for mutations in this gene. The gene shows tolerance to loss-of-function variants, consistent with the redundancy typical of the large olfactory receptor gene family.

ResearchSummary from RefSeq, UniProt, Mechanism

MultiplemechanismLOEUF 1.44

Clinical Summary— OR13D1

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Population Constraint (gnomAD)

Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

36 unique Pathogenic / Likely Pathogenic· 43 VUS of 87 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

1.44LOEUF

pLI 0.006

Z-score 0.83

OE 0.64 (0.31–1.44)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint

-0.48Z-score

OE missense 1.10 (0.98–1.24)

192 obs / 174.2 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios

LoF OE0.64 (0.31–1.44)

0≤0.351.4

Missense OE1.10 (0.98–1.24)

0≤0.61.4

Synonymous OE1.03

0≤1.21.6

LoF obs/exp: 4 / 6.2Missense obs/exp: 192 / 174.2Syn Z: -0.20

0.87top 5%

GOF

0.85top 5%

LOF

0.1499th %ile

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

DNprediction above median

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.