OLFML2B

protein-coding

olfactomedin like 2B

Gene summary

This gene encodes an olfactomedin domain-containing protein. Most olfactomedin domain-containing proteins are secreted glycoproteins. [provided by RefSeq, Dec 2016]

MANE transcript

NM_015441.3

Inheritance

—

ClinVar variants

P:5U:124B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.77

Max pathogenic AF

—

Genomic locus

chr1:161,983,192-162,023,869

External References & Databases

Ensembl (ENSG00000162745)

Transcript & Mutation Effects

hg38 • Region Span ~40.7 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 OLFML2B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 121

not providedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015441.3. 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 clinvar	3 clinvar	5
missense		5 clinvar	122 clinvar	4 clinvar		131
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	5	124	5	3	137

Highest pathogenic variant AF is 0.000042163483

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015441.3	RefSeq	NP_056256.1	8	MANE Select
ENST00000294794.8	Ensembl	ENSP00000294794.3	8	MANE Select
NM_001297713.2	RefSeq	NP_001284642.1	8	Standard
NM_001347700.2	RefSeq	NP_001334629.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000294794
Coding exons: 8
Length: 40663
Individuals with no LoFs: 125552
Homozygous LoFs: 1
Heterozygous LoFs: 195
Defined: 125748
p: 0.000780

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0780	453	458	0.990	0.0000284	4835
Missense (PolyPhen)		152	165.7	0.91735		1720
Synonymous	0.373	197	204	0.967	0.0000140	1556
Loss of Function	1.29	27	35.3	0.765	0.00000210	345

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.00065	0.00064	rare
Ashkenazi Jewish	0.0014	0.0014	notable
East Asian	0.00022	0.00022	rare
Finnish	0.00042	0.00042	rare
European (Non-Finnish)	0.00086	0.00085	rare
South Asian	0.0012	0.0011	notable
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.199
RVIS EVS: 1.23
RVIS percentile EVS: 93.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.143

Gene Damage Prediction

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