OBP2A

odorant binding protein 2A, the group of Lipocalins

Basic information

Region (hg38): 9:135546126-135549969

Links

ENSG00000122136 ∙ NCBI:29991 ∙ OMIM:164320 ∙ HGNC:23380 ∙ Uniprot:Q9NY56 ∙ 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 OBP2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OBP2A 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			13	2		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in OBP2A

This is a list of pathogenic ClinVar variants found in the OBP2A region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135546220-G-A		not specified	Uncertain significance (Oct 04, 2024)
9-135546220-G-T		not specified	Uncertain significance (Nov 30, 2021)
9-135546854-C-T		not specified	Uncertain significance (Apr 24, 2024)
9-135546872-C-A		not specified	Uncertain significance (Jun 11, 2021)
9-135546878-G-T		not specified	Uncertain significance (Feb 28, 2023)
9-135547182-G-A		not specified	Uncertain significance (Jan 17, 2024)
9-135547189-G-A		not specified	Uncertain significance (Feb 03, 2022)
9-135547227-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-135547230-C-T		not specified	Uncertain significance (Sep 25, 2024)
9-135547244-C-A		not specified	Uncertain significance (Feb 23, 2023)
9-135547246-C-A		not specified	Uncertain significance (May 24, 2024)
9-135547877-G-A		not specified	Uncertain significance (Apr 09, 2024)
9-135547884-G-T		not specified	Uncertain significance (Aug 30, 2022)
9-135547961-G-A		not specified	Uncertain significance (Sep 30, 2022)
9-135547978-G-A		not specified	Likely benign (Nov 21, 2024)
9-135548757-G-T		not specified	Likely benign (Feb 22, 2023)
9-135548765-A-G		not specified	Likely benign (Sep 29, 2022)
9-135548768-A-T		not specified	Uncertain significance (Apr 27, 2024)
9-135548770-G-A		not specified	Uncertain significance (Dec 27, 2023)
9-135549319-C-A		not specified	Uncertain significance (Apr 21, 2022)
9-135549322-G-A		not specified	Uncertain significance (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OBP2A	protein_coding	protein_coding	ENST00000539850	6	3831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000152	0.240	125627	0	114	125741	0.000453

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0311	102	101	1.01	0.00000629	1086
Missense in Polyphen		23	25.651	0.89667		349
Synonymous	-0.910	51	43.4	1.18	0.00000296	318
Loss of Function	0.0686	9	9.22	0.976	3.89e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00576	0.00576
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000546	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.0000546	0.0000544
South Asian	0.0000670	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably binds and transports small hydrophobic volatile molecules with a higher affinity for aldehydes and large fatty acids. {ECO:0000269|PubMed:12044155}.

Recessive Scores

• pRec: 0.0802

Intolerance Scores

• loftool: 0.649
• rvis_EVS: 1.33
• rvis_percentile_EVS: 94.13

Haploinsufficiency Scores

• pHI: 0.0523
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0277

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Obp2b

Gene ontology

• Biological process: sensory perception of chemical stimulus;sensory perception of smell;response to stimulus
• Cellular component: cellular_component;extracellular region
• Molecular function: odorant binding;small molecule binding