BIVM

basic, immunoglobulin-like variable motif containing

Basic information

Region (hg38): 13:102799119-102841533

Links

ENSG00000134897 ∙ NCBI:54841 ∙ OMIM:619006 ∙ HGNC:16034 ∙ Uniprot:Q86UB2 ∙ 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 BIVM gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIVM 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				1	1	2
missense			3	2		5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	3	1

Variants in BIVM

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

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

Position	Type	Phenotype	Significance	ClinVar
13-102807322-A-G		not specified	Uncertain significance (Feb 28, 2024)
13-102807503-C-T		not specified	Uncertain significance (Apr 07, 2023)
13-102807511-A-G		not specified	Benign/Likely benign (Aug 01, 2024)
13-102807561-C-T			Likely benign (Nov 20, 2018)
13-102839742-G-A			Benign (Nov 20, 2018)
13-102839783-C-T			Likely benign (Jul 01, 2024)
13-102839828-G-C		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BIVM	protein_coding	protein_coding	ENST00000257336	9	42487

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000187	0.999	125705	0	43	125748	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.737	235	269	0.874	0.0000137	3286
Missense in Polyphen		76	111.76	0.68002		1399
Synonymous	0.919	87	98.6	0.882	0.00000522	931
Loss of Function	2.87	11	27.1	0.406	0.00000133	339

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000226	0.000226
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000289	0.000277
European (Non-Finnish)	0.000239	0.000237
Middle Eastern	0.000109	0.000109
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.228
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.16

Haploinsufficiency Scores

• pHI: 0.207
• hipred: N
• hipred_score: 0.267
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.206

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bivm

Gene ontology

• Cellular component: extracellular space;nucleus;cytoplasm