RECQL

RecQ like helicase, the group of RecQ like helicases

Basic information

Region (hg38): 12:21468909-21501669

Links

ENSG00000004700 ∙ NCBI:5965 ∙ OMIM:600537 ∙ HGNC:9948 ∙ Uniprot:P46063 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• breast cancer (Disputed Evidence), mode of inheritance: AD
• RECON progeroid syndrome (Limited), mode of inheritance: AR
• familial ovarian cancer (No Known Disease Relationship), mode of inheritance: AD
• hereditary breast carcinoma (Disputed Evidence), mode of inheritance: AD

ClinVar

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

• Hereditary cancer-predisposing syndrome (943 variants)
• not provided (689 variants)
• not specified (17 variants)
• Hereditary breast ovarian cancer syndrome (9 variants)
• RECQL-related condition (8 variants)
• Inborn genetic diseases (6 variants)
• Hereditary cancer (5 variants)
• RECON progeroid syndrome (4 variants)
• Abnormal facial shape;Short stature (1 variants)
• Familial cancer of breast (1 variants)
• Seizure (1 variants)
• Malignant neoplastic disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RECQL 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				210	2	212
missense			678	10	3	691
nonsense		3	36			39
start loss						0
frameshift		2	65			67
inframe indel			17			17
splice donor/acceptor (+/-2bp)		4	18			22
splice region			31	25	8	64
non coding			9	84	57	150
Total	0	9	823	304	62

Highest pathogenic variant AF is 0.0000131

Variants in RECQL

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

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

Position	Type	Phenotype	Significance	ClinVar
12-21468957-T-C			Benign (Jul 09, 2018)
12-21469761-A-G			Benign (Jun 20, 2018)
12-21469812-C-T			Likely benign (Jun 26, 2018)
12-21469888-T-C			Likely benign (Jun 18, 2018)
12-21469993-T-C			Benign (Jun 18, 2018)
12-21470002-A-G			Likely benign (Nov 23, 2018)
12-21470188-T-G			Benign (Dec 15, 2017)
12-21470193-A-C			Likely benign (Jul 27, 2021)
12-21470195-C-T			Likely benign (Jan 27, 2022)
12-21470197-G-C			Likely benign (May 27, 2022)
12-21470200-A-G		not specified	Likely benign (Apr 19, 2021)
12-21470205-C-T			Uncertain significance (Jul 26, 2023)
12-21470206-G-A		not specified	Likely benign (Nov 28, 2022)
12-21470207-ATTTTTC-A		not specified	Uncertain significance (Nov 04, 2022)
12-21470207-A-AT		not specified	Uncertain significance (Sep 22, 2022)
12-21470213-C-A		not specified	Uncertain significance (Jun 03, 2023)
12-21470214-T-C			Uncertain significance (Jan 20, 2020)
12-21470222-G-A		not specified	Uncertain significance (Feb 29, 2024)
12-21470222-G-C		not specified	Uncertain significance (Jul 01, 2023)
12-21470224-T-G		not specified	Likely benign (Jan 14, 2023)
12-21470225-C-T		not specified	Uncertain significance (Jul 07, 2022)
12-21470226-C-T		not specified	Uncertain significance (Jul 27, 2023)
12-21470228-G-T			Uncertain significance (Jan 18, 2024)
12-21470231-T-A			Uncertain significance (Nov 01, 2022)
12-21470237-G-A		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RECQL	protein_coding	protein_coding	ENST00000444129	14	32759

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.53e-20	0.00279	125378	1	363	125742	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.249	322	335	0.962	0.0000167	4290
Missense in Polyphen		131	130.17	1.0063		1616
Synonymous	-0.375	121	116	1.04	0.00000649	1140
Loss of Function	0.160	31	32.0	0.970	0.00000149	428

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00128	0.00127
Ashkenazi Jewish	0.000797	0.000794
East Asian	0.000943	0.000925
Finnish	0.000564	0.000554
European (Non-Finnish)	0.00112	0.00111
Middle Eastern	0.000943	0.000925
South Asian	0.00618	0.00544
Other	0.00123	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: DNA helicase that may play a role in the repair of DNA that is damaged by ultraviolet light or other mutagens. Exhibits a magnesium-dependent ATP-dependent DNA-helicase activity that unwinds single- and double-stranded DNA in a 3'-5' direction. {ECO:0000269|PubMed:15886194, ECO:0000269|PubMed:7961977, ECO:0000269|PubMed:8056767}.

Recessive Scores

• pRec: 0.290

Intolerance Scores

• loftool: 0.990
• rvis_EVS: -0.97
• rvis_percentile_EVS: 8.9

Haploinsufficiency Scores

• pHI: 0.966
• hipred: Y
• hipred_score: 0.506
• ghis: 0.672

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Recql
• Phenotype: cellular phenotype

Gene ontology

• Biological process: double-strand break repair via homologous recombination;DNA strand renaturation;DNA repair;DNA recombination;DNA duplex unwinding
• Cellular component: nucleus;nucleoplasm;chromosome;cytoplasm;membrane
• Molecular function: DNA binding;DNA helicase activity;ATP-dependent DNA helicase activity;protein binding;ATP binding;four-way junction helicase activity;annealing helicase activity;ATP-dependent 3'-5' DNA helicase activity