OLFM4

Chr 13

olfactomedin 4

Also known as: GC1, GW112, OLM4, OlfD, UNQ362, bA209J19.1, hGC-1, hOLfD

NCBI Gene: 10562 ENSG00000102837 UniProt: Q6UX06

The protein is an extracellular matrix glycoprotein that facilitates cell adhesion and regulates cell proliferation and apoptosis. Mutations in this gene have been associated with neurodevelopmental disorders, though the specific phenotypic spectrum is still being characterized. The gene shows low constraint against loss-of-function variants (pLI near 0, LOEUF >1), suggesting tolerance to protein-truncating mutations.

ResearchSummary from RefSeq, UniProt

This gene was originally cloned from human myeloblasts and found to be selectively expressed in inflammed colonic epithelium. This gene encodes a member of the olfactomedin family. The encoded protein is an antiapoptotic factor that promotes tumor growth and is an extracellular matrix glycoprotein that facilitates cell adhesion. [provided by RefSeq, Mar 2011]

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.10

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.10LOEUF

pLI 0.000

Z-score 1.26

OE 0.67 (0.42–1.10)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.34Z-score

OE missense 0.94 (0.85–1.04)

264 obs / 280.1 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.67 (0.42–1.10)

0≤0.351.4

Missense OE?0.94 (0.85–1.04)

0≤0.61.4

Synonymous OE?1.06

0≤1.21.6

LoF obs/exp: 11 / 16.5Missense obs/exp: 264 / 280.1Syn Z: -0.52

Background carrier burden — how many people carry a rare variant somewhere in OLFM4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 71

642 rare PASS variants

Rare truncating (LoF)

1 in 1,900

75 rare PASS variants

Rare synonymous (reference)

1 in 130

270 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for OLFM4. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 110	1 in 2,200
South Asian	~43k	1 in 110	1 in 3,300
Remaining (unassigned)	~30k	1 in 100	1 in 1,700
European (Finnish)	~27k	1 in 520	1 in 5,300
Admixed American	~22k	1 in 67	1 in 430
African / African American	~21k	1 in 110	1 in 900
East Asian	~20k	1 in 110	1 in 1,000
Ashkenazi Jewish	~13k	1 in 370	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 97	≈ 1 in 720

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): All 5 coding exons well covered in gnomAD exomes and genomes.? see exons ↓