BIVM-ERCC5

protein-coding

BIVM-ERCC5 readthrough

Gene summary

This locus represents naturally occurring read-through transcription between the neighboring BIVM (basic, immunoglobulin-like variable motif containing) and ERCC5 (excision repair cross-complementing rodent repair deficiency, complementation group 5) genes on chromosome 13. The read-through transcript encodes a fusion protein that shares sequence identity with the products of each individual gene. [provided by RefSeq, Feb 2011]

MANE transcript

N/A

Inheritance

—

ClinVar variants

P:43U:144B:114

Top phenotype

Xeroderma pigmentosum, group G

gnomAD constraint

pLI —, LoF o/e 0.52

Max pathogenic AF

—

Genomic locus

chr13:102,799,110-102,875,994

External References & Databases

Ensembl (ENSG00000270181)

NCBI Gene (100533467)

Transcript & Mutation Effects

hg38 • Region Span ~76.9 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-ERCC5 variants in ClinVar

16 Conditions Cataloged

not providedTotal: 251

Xeroderma pigmentosum, group GTotal: 131

Hereditary cancer-predisposing syndromeTotal: 72

not specifiedTotal: 64

Cerebrooculofacioskeletal syndrome 3Total: 26

Inborn genetic diseasesTotal: 19

Xeroderma pigmentosumTotal: 12

Ovarian cancerTotal: 10

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . 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			10 clinvar	64 clinvar	6 clinvar	80
missense	3 clinvar	5 clinvar	122 clinvar	31 clinvar	8 clinvar	169
nonsense	5 clinvar	5 clinvar	2 clinvar			12
start loss						0
frameshift	13 clinvar	8 clinvar	3 clinvar			24
splice donor/acceptor (+/-2bp)	1 clinvar	3 clinvar	7 clinvar	3 clinvar	2 clinvar	16
Total	22	21	144	98	16	301

Highest pathogenic variant AF is 0.0000394291

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 5 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001204425.2	RefSeq	NP_001191354.2	23	Standard
ENST00000638434.1	Ensembl	ENSP00000492455.1	5	Standard
ENST00000639118.1	Ensembl	ENSP00000492444.1	5	Standard
ENST00000639132.1	Ensembl	ENSP00000492684.1	21	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nucleotide excision repair - Homo sapiens (human)

Biological Process

nucleotide-excision repair, DNA incision, 3'-to lesion

Molecular Function

single-stranded DNA binding
endodeoxyribonuclease activity

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000602836
Coding exons: 21
Length: 65045
Individuals with no LoFs: 125664
Homozygous LoFs: 0
Heterozygous LoFs: 84
Defined: 125748
p: 0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.602	691	737	0.938	0.0000408	9106
Missense (PolyPhen)		265	300.98	0.88045		3663
Synonymous	0.990	256	277	0.924	0.0000167	2601
Loss of Function	3.65	36	68.6	0.525	0.00000351	847

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00028	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00015	0.00014	rare
European (Non-Finnish)	0.00039	0.00039	rare
South Asian	0.00065	0.00065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP