OLFML2B

olfactomedin like 2B

Basic information

Region (hg38): 1:161983192-162023869

Links

ENSG00000162745 ∙ NCBI:25903 ∙ ∙ HGNC:24558 ∙ Uniprot:Q68BL8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OLFML2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OLFML2B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			50	2		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	50	2	3

Variants in OLFML2B

This is a list of pathogenic ClinVar variants found in the OLFML2B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-161983694-T-A		not specified	Uncertain significance (Oct 30, 2023)
1-161983763-G-T		not specified	Uncertain significance (Mar 18, 2024)
1-161983785-C-T		not specified	Uncertain significance (Jun 17, 2022)
1-161983898-A-C		not specified	Uncertain significance (May 30, 2023)
1-161983907-C-T			Likely pathogenic (Aug 01, 2015)
1-161983922-C-T		not specified	Uncertain significance (Jan 18, 2023)
1-161983934-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-161983955-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-161983968-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-161984016-C-T		not specified	Uncertain significance (Jun 04, 2024)
1-161984018-T-C		not specified	Uncertain significance (Jan 26, 2022)
1-161984140-A-G			Benign (Jun 21, 2018)
1-161984177-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-161984190-C-A		not specified	Uncertain significance (Jul 05, 2023)
1-161984226-G-A		not specified	Uncertain significance (Aug 28, 2023)
1-161984259-A-G			Uncertain significance (Mar 01, 2022)
1-161984843-T-C		not specified	Uncertain significance (Apr 01, 2024)
1-161984849-C-T			Likely pathogenic (Aug 01, 2015)
1-161984867-C-A		not specified	Uncertain significance (Jun 24, 2022)
1-161984875-C-T		not specified	Uncertain significance (Aug 15, 2023)
1-161984884-T-A		not specified	Uncertain significance (Apr 17, 2024)
1-161984911-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-161984950-G-A		not specified	Uncertain significance (Mar 18, 2024)
1-161984980-C-T		not specified	Uncertain significance (Oct 26, 2021)
1-161997828-T-C		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OLFML2B	protein_coding	protein_coding	ENST00000294794	8	40663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.65e-15	0.264	125552	1	195	125748	0.000780

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0780	453	458	0.990	0.0000284	4835
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00138
Ashkenazi Jewish	0.00140	0.00139
East Asian	0.000218	0.000217
Finnish	0.000417	0.000416
European (Non-Finnish)	0.000861	0.000853
Middle Eastern	0.000218	0.000217
South Asian	0.00121	0.00114
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.199
• rvis_EVS: 1.23
• rvis_percentile_EVS: 93.26

Haploinsufficiency Scores

• pHI: 0.281
• hipred: N
• hipred_score: 0.453
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.143

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfml2b

Gene ontology

• Cellular component: extracellular region