BIVM

protein-coding

basic, immunoglobulin-like variable motif containing

Gene summary

Predicted to enable DNA endonuclease activity and single-stranded DNA binding activity. Predicted to be involved in DNA metabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017693.4

Inheritance

—

ClinVar variants

U:10B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr13:102,799,119-102,841,533

External References & Databases

Ensembl (ENSG00000134897)

Transcript & Mutation Effects

hg38 • Region Span ~42.4 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 BIVM variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 12

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017693.4. 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	2
missense			10 clinvar	2 clinvar	1 clinvar	13
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	3	2	15

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 136 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017693.4	RefSeq	NP_060163.2	9	MANE Select
ENST00000257336.6	Ensembl	ENSP00000257336.1	9	MANE Select
NM_001159596.2	RefSeq	NP_001153068.1	7	Standard
ENST00000448849.3	Ensembl	ENSP00000412794.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular space
nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000257336
Coding exons: 9
Length: 42487
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125748
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.737	235	269	0.874	0.0000137	3286
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.00016	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00029	0.00028	rare
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.228
RVIS EVS: -0.18
RVIS percentile EVS: 40.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.206

Gene Damage Prediction

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