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.

not_specified (126 variants)
not_provided (1 variants)

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. These statistics are base on transcript: NM_000014881.5. 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						0
missense			112 clinvar	14 clinvar		126
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	112	14	0

Loading clinvar variants...

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