OBP2B

odorant binding protein 2B, the group of Lipocalins

Basic information

Region (hg38): 9:133205277-133209250

Links

ENSG00000171102 ∙ NCBI:29989 ∙ OMIM:604606 ∙ HGNC:23381 ∙ Uniprot:Q9NPH6 ∙ 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 OBP2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OBP2B 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						0
missense			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in OBP2B

This is a list of pathogenic ClinVar variants found in the OBP2B region.

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

Position	Type	Phenotype	Significance	ClinVar
9-133205926-C-G		not specified	Uncertain significance (Mar 06, 2023)
9-133205936-G-C		not specified	Uncertain significance (Jan 23, 2024)
9-133206329-G-A		not specified	Likely benign (Jan 26, 2022)
9-133206379-T-A		not specified	Uncertain significance (Dec 22, 2023)
9-133207240-A-G		not specified	Uncertain significance (Jun 17, 2024)
9-133208159-G-A		not specified	Uncertain significance (Apr 06, 2024)
9-133208166-G-A		not specified	Uncertain significance (Sep 29, 2023)
9-133208549-C-A		not specified	Uncertain significance (Jan 26, 2022)
9-133208553-G-A		not specified	Uncertain significance (Jun 22, 2024)
9-133208553-G-C		not specified	Uncertain significance (Nov 21, 2023)
9-133208566-C-T		not specified	Uncertain significance (Jun 02, 2023)
9-133209174-G-A		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OBP2B	protein_coding	protein_coding	ENST00000372034	6	3967

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000132	0.404	125642	1	101	125744	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.250	93	100	0.930	0.00000577	1101
Missense in Polyphen		17	19.777	0.85959		274
Synonymous	-0.756	52	45.5	1.14	0.00000303	315
Loss of Function	0.370	8	9.21	0.868	3.88e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000662	0.000610
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000144	0.000139
European (Non-Finnish)	0.000758	0.000747
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably binds and transports small hydrophobic volatile molecules.

Intolerance Scores

• rvis_EVS: 0.59
• rvis_percentile_EVS: 82.51

Haploinsufficiency Scores

• pHI: 0.0745
• hipred: N
• hipred_score: 0.195

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.631

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Obp2a
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); pigmentation phenotype

Gene ontology

• Biological process: sensory perception of smell;chemosensory behavior
• Cellular component: cellular_component;extracellular region
• Molecular function: odorant binding;small molecule binding