OLFM4

protein-coding

olfactomedin 4

Gene summary

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]

MANE transcript

NM_006418.5

Inheritance

—

ClinVar variants

U:65B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr13:53,028,813-53,052,057

External References & Databases

Ensembl (ENSG00000102837)

Transcript & Mutation Effects

hg38 • Region Span ~23.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OLFM4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 71

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006418.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			65 clinvar	5 clinvar		70
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	6	0	71

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006418.5	RefSeq	NP_006409.3	5	MANE Select
ENST00000219022.3	Ensembl	ENSP00000219022.2	5	MANE Select
ENST00001131483.1	Ensembl	ENSP00000801626.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

cell adhesion
regulation of necrotic cell death
regulation of apoptotic process
neutrophil degranulation
regulation of phagocytosis

Molecular Function

catalytic activity
protein binding
protein homodimerization activity
cadherin binding

Cellular Component

extracellular region
extracellular space
mitochondrion
plasma membrane
secretory granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000219022
Coding exons: 5
Length: 23299
Individuals with no LoFs: 122409
Homozygous LoFs: 55
Heterozygous LoFs: 3284
Defined: 125748
p: 0.0134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.342	264	280	0.942	0.0000150	3350
Missense (PolyPhen)		79	92.166	0.85715		1157
Synonymous	-0.523	119	112	1.06	0.00000622	1009
Loss of Function	1.26	11	16.5	0.665	8.53e-7	215

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0026	0.0026	notable
Latino/Admixed American	0.0057	0.0057	notable
Ashkenazi Jewish	0.0052	0.0052	notable
East Asian	0.00044	0.00044	rare
Finnish	0.058	0.058	notable
European (Non-Finnish)	0.015	0.015	notable
South Asian	0.0016	0.0016	notable
Other	0.014	0.014	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May promote proliferation of pancreatic cancer cells by favoring the transition from the S to G2/M phase. In myeloid leukemic cell lines, inhibits cell growth and induces cell differentiation and apoptosis. May play a role in the inhibition of EIF4EBP1 phosphorylation/deactivation. Facilitates cell adhesion, most probably through interaction with cell surface lectins and cadherin. {ECO:0000269|PubMed:16566923, ECO:0000269|PubMed:17270022, ECO:0000269|PubMed:20724538}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.246
RVIS EVS: 0.53
RVIS percentile EVS: 80.96

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.262

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium