OLFM3

protein-coding

olfactomedin 3

Gene summary

Predicted to be involved in signal transduction. Predicted to be located in Golgi apparatus; extracellular region; and synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_058170.4

Inheritance

—

ClinVar variants

U:52B:2

Top phenotype

Strabismus, susceptibility to

gnomAD constraint

pLI —, LoF o/e 0.39

Max pathogenic AF

—

Genomic locus

chr1:101,802,560-101,996,926

External References & Databases

Ensembl (ENSG00000118733)

Transcript & Mutation Effects

hg38 • Region Span ~194.4 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 OLFM3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 50

not providedTotal: 2

Strabismus, susceptibility toTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_058170.4. 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				2 clinvar		2
missense			51 clinvar			51
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	52	2	0	54

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_058170.4	RefSeq	NP_477518.2	6	MANE Select
ENST00000370103.9	Ensembl	ENSP00000359121.5	6	MANE Select
NM_001288821.2	RefSeq	NP_001275750.1	6	Standard
NM_001288823.2	RefSeq	NP_001275752.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

eye photoreceptor cell development

Molecular Function

protein binding

Cellular Component

extracellular space
Golgi apparatus
cell junction
AMPA glutamate receptor complex
synapse

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000370103
Coding exons: 6
Length: 194457
Individuals with no LoFs: 125733
Homozygous LoFs: 0
Heterozygous LoFs: 15
Defined: 125748
p: 0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.61	174	245	0.710	0.0000120	3032
Missense (PolyPhen)		79	124.46	0.63474		1533
Synonymous	-2.05	115	90.2	1.27	0.00000432	844
Loss of Function	2.68	9	22.8	0.394	0.00000128	258

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.122

Intolerance Scores

LoFtool: 0.279
RVIS EVS: -0.76
RVIS percentile EVS: 13.33

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.853

Gene Damage Prediction

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