RECQL5

RecQ like helicase 5, the group of RecQ like helicases

Basic information

Region (hg38): 17:75626844-75667189

Links

ENSG00000108469 ∙ NCBI:9400 ∙ OMIM:603781 ∙ HGNC:9950 ∙ Uniprot:O94762 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• coronary artery disorder (Limited), mode of inheritance: AR
• breast cancer (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RECQL5 gene.

• Inborn genetic diseases (62 variants)
• not provided (17 variants)
• RECQL5-related condition (16 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RECQL5 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				4	1	5
missense			60	7	7	74
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)				1		1
splice region					2	2
non coding			9	1		10
Total	0	0	70	13	8

Variants in RECQL5

This is a list of pathogenic ClinVar variants found in the RECQL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75627448-G-A		RECQL5-related disorder	Uncertain significance (Feb 12, 2024)
17-75627462-C-T		RECQL5-related disorder • not specified	Uncertain significance (Mar 01, 2024)
17-75627467-G-A		RECQL5-related disorder	Likely benign (Jan 23, 2024)
17-75627473-G-A		RECQL5-related disorder	Likely benign (Aug 04, 2022)
17-75627526-C-T		RECQL5-related disorder	Likely benign (Sep 08, 2022)
17-75627617-G-A			Benign (Dec 31, 2019)
17-75627670-C-T		RECQL5-related disorder	Benign (Nov 16, 2019)
17-75627671-G-A		not specified	Uncertain significance (Feb 17, 2022)
17-75627673-G-A		not specified	Uncertain significance (Nov 30, 2022)
17-75627681-T-A		not specified	Uncertain significance (Dec 15, 2023)
17-75627694-T-C			Likely benign (Dec 31, 2019)
17-75628268-C-T		not specified	Uncertain significance (Jan 26, 2023)
17-75628270-A-G		not specified	Uncertain significance (Feb 21, 2024)
17-75628273-T-G		RECQL5-related disorder	Likely benign (Feb 28, 2022)
17-75628279-G-A		not specified	Uncertain significance (Oct 05, 2023)
17-75628295-C-T		RECQL5-related disorder	Uncertain significance (Nov 28, 2022)
17-75628304-C-T		not specified	Uncertain significance (Nov 15, 2021)
17-75628306-G-C		not specified	Uncertain significance (Dec 19, 2022)
17-75628307-A-G		not specified	Likely benign (Mar 27, 2023)
17-75628327-G-C		not specified	Uncertain significance (Dec 19, 2022)
17-75628354-C-G		not specified	Uncertain significance (Sep 26, 2022)
17-75628385-C-T		RECQL5-related disorder	Likely benign (Dec 01, 2022)
17-75628386-G-A		RECQL5-related disorder	Benign (Dec 16, 2019)
17-75628388-C-T		RECQL5-related disorder	Uncertain significance (Jan 12, 2024)
17-75628392-G-C		RECQL5-related disorder	Likely benign (Jan 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RECQL5	protein_coding	protein_coding	ENST00000317905	19	40345

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.17e-18	0.381	125660	0	88	125748	0.000350

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00455	577	577	1.00	0.0000357	6399
Missense in Polyphen		154	169.66	0.9077		1873
Synonymous	0.215	227	231	0.982	0.0000143	1985
Loss of Function	1.68	34	46.3	0.734	0.00000235	549

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000745	0.000735
Ashkenazi Jewish	0.00	0.00
East Asian	0.000221	0.000217
Finnish	0.000477	0.000462
European (Non-Finnish)	0.000372	0.000316
Middle Eastern	0.000221	0.000217
South Asian	0.000622	0.000621
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Isoform beta is a DNA helicase that plays an important role in DNA replication, transcription and repair. Inhibits elongation of stalled transcripts at DNA damage sites by binding to the RNA polymerase II subunit POLR2A and blocking the TCEA1 binding site. Required for mitotic chromosome separation after cross-over events and cell cycle progress. Required for efficient DNA repair, including repair of inter-strand cross-links. Stimulates DNA decatenation mediated by TOP2A. Prevents sister chromatid exchange and homologous recombination. {ECO:0000269|PubMed:20231364, ECO:0000269|PubMed:20348101, ECO:0000269|PubMed:20643585, ECO:0000269|PubMed:22013166, ECO:0000269|PubMed:22973052, ECO:0000269|PubMed:23715498, ECO:0000269|PubMed:23748380}.

Recessive Scores

• pRec: 0.226

Intolerance Scores

• loftool: 0.891
• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.68

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.663
• ghis: 0.509

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.575

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Recql5
• Phenotype: cellular phenotype

Gene ontology

• Biological process: mitotic sister chromatid segregation;mitotic cell cycle;double-strand break repair via homologous recombination;DNA metabolic process;DNA replication;DNA repair;DNA recombination;response to X-ray;DNA duplex unwinding;negative regulation of transcription elongation from RNA polymerase II promoter;negative regulation of mitotic cell cycle;cell division;chromosome separation;cellular response to camptothecin;replication-born double-strand break repair via sister chromatid exchange;negative regulation of double-strand break repair via homologous recombination
• Cellular component: nucleus;nucleoplasm;chromosome;cytoplasm;cytosol;RNA polymerase II, holoenzyme
• Molecular function: RNA polymerase II complex binding;DNA binding;DNA helicase activity;ATP binding;four-way junction helicase activity;identical protein binding;ATP-dependent 3'-5' DNA helicase activity