OLFML2A

protein-coding

olfactomedin like 2A

Gene summary

Predicted to enable extracellular matrix binding activity and identical protein binding activity. Predicted to be involved in signal transduction. Predicted to act upstream of or within extracellular matrix organization. Predicted to be located in extracellular matrix. Predicted to be active in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_182487.4

Inheritance

—

ClinVar variants

U:175B:8

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr9:124,777,133-124,814,885

External References & Databases

Ensembl (ENSG00000185585)

Transcript & Mutation Effects

hg38 • Region Span ~37.8 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 OLFML2A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 174

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182487.4. 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			1 clinvar			1
missense			173 clinvar	8 clinvar		181
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	175	8	0	183

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182487.4	RefSeq	NP_872293.2	8	MANE Select
ENST00000373580.8	Ensembl	ENSP00000362682.3	8	MANE Select
NM_001282715.2	RefSeq	NP_001269644.1	5	Standard
ENST00000288815.5	Ensembl	ENSP00000288815.5	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

extracellular matrix organization

Molecular Function

protein homodimerization activity
extracellular matrix binding

Cellular Component

extracellular matrix

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373580
Coding exons: 8
Length: 37728
Individuals with no LoFs: 125597
Homozygous LoFs: 0
Heterozygous LoFs: 151
Defined: 125748
p: 0.000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.360	442	421	1.05	0.0000286	4217
Missense (PolyPhen)		108	107.33	1.0062		1060
Synonymous	0.721	178	191	0.934	0.0000142	1341
Loss of Function	1.58	18	26.8	0.672	0.00000138	297

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00038	0.00038	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00071	0.00071	rare
Finnish	0.00037	0.00037	rare
European (Non-Finnish)	0.00083	0.00083	rare
South Asian	0.00043	0.00042	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.197
RVIS EVS: -0.73
RVIS percentile EVS: 14.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.945

Gene Damage Prediction

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