BIVM-ERCC5

BIVM-ERCC5 readthrough

Basic information

Region (hg38): 13:102799110-102875994

Links

ENSG00000270181

∙ NCBI:100533467 ∙ ∙ HGNC:43690 ∙ ∙ ∙ 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-ERCC5 gene.

not provided (251 variants)
Xeroderma pigmentosum, group G (131 variants)
Hereditary cancer-predisposing syndrome (72 variants)
not specified (64 variants)
Cerebrooculofacioskeletal syndrome 3 (26 variants)
Inborn genetic diseases (19 variants)
Xeroderma pigmentosum (12 variants)
Ovarian cancer (10 variants)
Cerebrooculofacioskeletal syndrome 3;Xeroderma pigmentosum, group G (7 variants)
Xeroderma pigmentosum group G/Cockayne syndrome (4 variants)
Xeroderma pigmentosum, group G;Cerebrooculofacioskeletal syndrome 3 (4 variants)
Xeroderma pigmentosum-Cockayne syndrome complex (1 variants)
See cases (1 variants)
ERCC5-related condition (1 variants)
8 conditions (1 variants)
Hepatoblastoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BIVM-ERCC5 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	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

Highest pathogenic variant AF is 0.0000394291

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BIVM-ERCC5	protein_coding	protein_coding	ENST00000602836	21	65045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.28e-15	1.00	125664	0	84	125748	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.602	691	737	0.938	0.0000408	9106
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000527	0.000527
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000149	0.000139
European (Non-Finnish)	0.000389	0.000387
Middle Eastern	0.000218	0.000217
South Asian	0.000654	0.000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Pathway: Nucleotide excision repair - Homo sapiens (human) (Consensus)

Gene ontology

Biological process: nucleotide-excision repair, DNA incision, 3'-to lesion
Cellular component: nucleus
Molecular function: single-stranded DNA binding;endodeoxyribonuclease activity