BIVM-ERCC5

BIVM-ERCC5 readthrough

Basic information

Region (hg38): 13:102799109-102875994

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.

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			10	64	6	80
missense	3	5	122	31	8	169
nonsense	5	5	2			12
start loss						0
frameshift	13	8	3			24
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	3	7	3	2	16
splice region						0
non coding	1	1	16	26	41	85
Total	23	22	161	124	57

Highest pathogenic variant AF is 0.0000394

Variants in BIVM-ERCC5

This is a list of pathogenic ClinVar variants found in the BIVM-ERCC5 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 (Mar 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 (Mar 01, 2024)
13-102839828-G-C		not specified	Uncertain significance (Oct 26, 2022)
13-102845499-G-C			Benign (Apr 09, 2019)
13-102845549-G-A			Benign (Apr 03, 2019)
13-102845567-T-C			Benign (Jan 10, 2019)
13-102845721-C-T			Benign (Apr 03, 2019)
13-102845821-G-C			Benign (Apr 03, 2019)
13-102845827-A-C		Xeroderma pigmentosum	Likely benign (Jun 15, 2019)
13-102845830-C-A		Xeroderma pigmentosum	Benign/Likely benign (Feb 28, 2019)
13-102845848-A-G		Xeroderma pigmentosum, group G	Benign (Nov 11, 2018)
13-102845887-C-T		Xeroderma pigmentosum, group G	Uncertain significance (Jan 12, 2018)
13-102846025-T-C		Xeroderma pigmentosum, group G	Benign (Nov 11, 2018)
13-102846026-G-C		Xeroderma pigmentosum, group G	Uncertain significance (Jan 13, 2018)
13-102846067-G-C		Xeroderma pigmentosum, group G	Benign/Likely benign (Jun 01, 2023)
13-102846075-A-C		Xeroderma pigmentosum, group G	Uncertain significance (Apr 27, 2017)
13-102846111-C-A		Xeroderma pigmentosum, group G	Uncertain significance (Jan 12, 2018)
13-102846121-A-G		Xeroderma pigmentosum, group G	Uncertain significance (Jan 12, 2018)
13-102846141-A-G		Xeroderma pigmentosum, group G	Uncertain significance (Jan 13, 2018)
13-102846193-G-A		Xeroderma pigmentosum, group G	Benign (Apr 03, 2019)
13-102846195-C-T		Xeroderma pigmentosum, group G	Benign (Nov 11, 2018)

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