DCLRE1A

DNA cross-link repair 1A, the group of DNA cross-link repair family

Basic information

Region (hg38): 10:113834725-113854383

Links

ENSG00000198924 ∙ NCBI:9937 ∙ OMIM:609682 ∙ HGNC:17660 ∙ Uniprot:Q6PJP8 ∙ 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 DCLRE1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCLRE1A 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						0
missense			49	8		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	8	0

Variants in DCLRE1A

This is a list of pathogenic ClinVar variants found in the DCLRE1A region.

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

Position	Type	Phenotype	Significance	ClinVar
10-113835270-C-T		not specified	Uncertain significance (Feb 05, 2024)
10-113835271-G-A		not specified	Uncertain significance (Nov 22, 2023)
10-113835303-T-C		not specified	Uncertain significance (Nov 20, 2023)
10-113837106-A-G		not specified	Uncertain significance (Aug 23, 2021)
10-113841426-T-C		not specified	Uncertain significance (Jun 27, 2023)
10-113841486-G-A		not specified	Uncertain significance (May 06, 2022)
10-113841516-T-G		not specified	Uncertain significance (Feb 05, 2024)
10-113841557-A-G		not specified	Uncertain significance (Oct 20, 2023)
10-113842396-T-C		not specified	Likely benign (Feb 14, 2023)
10-113842427-T-C		not specified	Uncertain significance (Apr 25, 2023)
10-113842427-T-G		not specified	Uncertain significance (Feb 17, 2024)
10-113842439-A-G		not specified	Uncertain significance (Mar 25, 2024)
10-113844168-C-A		not specified	Uncertain significance (Feb 03, 2023)
10-113844204-C-A		not specified	Uncertain significance (Jul 26, 2022)
10-113845802-A-G		not specified	Uncertain significance (Oct 21, 2021)
10-113847212-T-A		not specified	Uncertain significance (Jun 27, 2022)
10-113847300-C-T		not specified	Likely benign (Dec 18, 2023)
10-113847309-G-C		not specified	Uncertain significance (Jun 22, 2023)
10-113847315-C-T		not specified	Uncertain significance (Jun 30, 2022)
10-113848994-T-C		not specified	Uncertain significance (Sep 20, 2023)
10-113849181-T-C		not specified	Likely benign (Jul 26, 2023)
10-113849261-C-T		not specified	Uncertain significance (Mar 01, 2024)
10-113849393-T-C		not specified	Uncertain significance (Sep 16, 2021)
10-113849423-A-C		not specified	Uncertain significance (Mar 07, 2024)
10-113849445-T-A		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCLRE1A	protein_coding	protein_coding	ENST00000361384	9	19655

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.94e-9	0.998	124966	6	776	125748	0.00311

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.579	499	537	0.930	0.0000267	6848
Missense in Polyphen		104	132	0.7879		1725
Synonymous	-0.0957	202	200	1.01	0.0000105	1955
Loss of Function	2.84	21	40.5	0.518	0.00000206	562

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00417	0.00417
Ashkenazi Jewish	0.00	0.00
East Asian	0.00240	0.00234
Finnish	0.00263	0.00259
European (Non-Finnish)	0.00431	0.00431
Middle Eastern	0.00240	0.00234
South Asian	0.00173	0.00170
Other	0.00310	0.00310

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be required for DNA interstrand cross-link repair. Also required for checkpoint mediated cell cycle arrest in early prophase in response to mitotic spindle poisons. {ECO:0000269|PubMed:15542852}.
• Pathway: Fanconi Anemia Pathway;DNA Repair (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.552
• rvis_EVS: 2.29
• rvis_percentile_EVS: 98.31

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.296
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.423

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dclre1a
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); neoplasm; immune system phenotype

Gene ontology

• Biological process: double-strand break repair via nonhomologous end joining;cell cycle;protection from non-homologous end joining at telomere;interstrand cross-link repair;cell division;nucleic acid phosphodiester bond hydrolysis
• Cellular component: nuclear chromosome, telomeric region;fibrillar center;nucleoplasm
• Molecular function: damaged DNA binding;5'-3' exodeoxyribonuclease activity