ERCC6L

ERCC excision repair 6 like, spindle assembly checkpoint helicase

Basic information

Region (hg38): X:72204656-72239027

Links

ENSG00000186871 ∙ NCBI:54821 ∙ OMIM:300687 ∙ HGNC:20794 ∙ Uniprot:Q2NKX8 ∙ 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 ERCC6L gene.

• Inborn genetic diseases (20 variants)
• not provided (6 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERCC6L 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				2	1	3
missense			19	2	2	23
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	4	3

Variants in ERCC6L

This is a list of pathogenic ClinVar variants found in the ERCC6L region.

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

Position	Type	Phenotype	Significance	ClinVar
X-72205067-G-A		not specified	Uncertain significance (Aug 15, 2023)
X-72205274-G-A		not specified	Uncertain significance (Oct 16, 2023)
X-72205325-C-T			Likely benign (-)
X-72205359-G-A			Likely benign (Mar 01, 2023)
X-72205470-A-T			Likely benign (Jul 01, 2022)
X-72205611-T-A		not specified	Uncertain significance (Feb 13, 2023)
X-72205942-G-T		not specified	Uncertain significance (Feb 07, 2023)
X-72205954-AACTTGGCCTC-A		not specified	Uncertain significance (Nov 17, 2016)
X-72206057-C-G		not specified	Uncertain significance (Jan 23, 2023)
X-72206081-A-C		not specified	Uncertain significance (Oct 04, 2022)
X-72206108-C-T		not specified	Uncertain significance (Sep 16, 2021)
X-72206231-C-G		not specified	Uncertain significance (Dec 19, 2022)
X-72206248-T-C		not specified	Uncertain significance (Mar 08, 2024)
X-72206437-A-G		not specified	Uncertain significance (Oct 03, 2022)
X-72206450-C-T		not specified	Uncertain significance (Jul 26, 2022)
X-72206509-T-C		not specified	Uncertain significance (Dec 05, 2022)
X-72206930-T-C		not specified	Uncertain significance (Dec 01, 2022)
X-72206972-C-G		not specified	Uncertain significance (Aug 16, 2022)
X-72207230-G-A		not specified	Uncertain significance (Mar 06, 2023)
X-72207313-G-A		not specified	Uncertain significance (Jan 26, 2022)
X-72207413-C-T		not specified	Uncertain significance (Dec 07, 2021)
X-72207574-C-T			Uncertain significance (-)
X-72207644-G-A		not specified	Uncertain significance (Dec 21, 2023)
X-72207740-C-G			Likely benign (Dec 01, 2022)
X-72207937-C-G		not specified	Uncertain significance (Aug 17, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERCC6L	protein_coding	protein_coding	ENST00000334463	2	34388

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000684	125619	6	17	125642	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.89	267	437	0.611	0.0000310	8275
Missense in Polyphen		43	125.58	0.34241		2351
Synonymous	1.41	142	165	0.860	0.0000120	2400
Loss of Function	4.72	2	29.9	0.0670	0.00000241	538

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000484	0.000441
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000625	0.0000462
European (Non-Finnish)	0.000147	0.000106
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000222	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA helicase that acts as an essential component of the spindle assembly checkpoint. Contributes to the mitotic checkpoint by recruiting MAD2 to kinetochores and monitoring tension on centromeric chromatin (PubMed:17218258). Acts as a tension sensor that associates with catenated DNA which is stretched under tension until it is resolved during anaphase (PubMed:17218258, PubMed:23973328). Functions as ATP-dependent DNA translocase (PubMed:23973328, PubMed:28977671). Can promote Holliday junction branch migration (in vitro) (PubMed:23973328). {ECO:0000269|PubMed:17218258, ECO:0000269|PubMed:23973328, ECO:0000269|PubMed:28977671}.
• Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;PLK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.0974

Intolerance Scores

• loftool: 0.0101
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.56

Haploinsufficiency Scores

• pHI: 0.337
• hipred: Y
• hipred_score: 0.809
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.583

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ercc6l

Gene ontology

• Biological process: cell cycle;cell division
• Cellular component: condensed chromosome kinetochore;cytosol;membrane
• Molecular function: DNA binding;helicase activity;protein binding;ATP binding;DNA translocase activity