HELQ

helicase, POLQ like, the group of DNA helicases

Basic information

Region (hg38): 4:83407342-83455855

Links

ENSG00000163312 ∙ NCBI:113510 ∙ OMIM:606769 ∙ HGNC:18536 ∙ Uniprot:Q8TDG4 ∙ 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 HELQ gene.

• Inborn genetic diseases (38 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HELQ 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			34	5	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	34	5	1

Variants in HELQ

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

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

Position	Type	Phenotype	Significance	ClinVar
4-83407479-C-T		HELQ-related disorder	Benign (Mar 15, 2019)
4-83407482-C-T		not specified	Uncertain significance (Apr 25, 2022)
4-83407544-T-C		not specified	Uncertain significance (Dec 18, 2023)
4-83416770-T-A		not specified	Uncertain significance (Nov 22, 2021)
4-83416804-T-C		not specified	Uncertain significance (Dec 01, 2022)
4-83416821-C-T		not specified	Uncertain significance (Jan 04, 2022)
4-83421603-C-G		not specified	Uncertain significance (Aug 16, 2022)
4-83421676-T-G		not specified	Uncertain significance (Oct 12, 2022)
4-83421714-T-C		not specified	Uncertain significance (Jun 21, 2022)
4-83421730-C-T		not specified	Uncertain significance (Jun 28, 2022)
4-83421744-G-C		HELQ-related disorder	Likely benign (Oct 28, 2019)
4-83426090-A-G		HELQ-related disorder	Likely benign (Jul 01, 2022)
4-83427592-T-C		not specified	Likely benign (Nov 03, 2022)
4-83427612-T-A		HELQ-related disorder	Benign (Mar 15, 2019)
4-83427619-T-C		not specified	Uncertain significance (Mar 01, 2023)
4-83427715-T-C		not specified	Uncertain significance (Feb 28, 2024)
4-83429553-A-G		not specified	Uncertain significance (Feb 16, 2023)
4-83429623-T-C		not specified	Uncertain significance (Feb 23, 2023)
4-83429625-A-G		not specified	Uncertain significance (Dec 27, 2023)
4-83429687-C-T		HELQ-related disorder	Benign (Apr 09, 2019)
4-83429717-A-G		HELQ-related disorder	Benign (Nov 14, 2019)
4-83432201-A-C		HELQ-related disorder	Likely benign (Oct 25, 2019)
4-83432241-G-C		not specified	Uncertain significance (Feb 05, 2024)
4-83436918-A-G		not specified	Uncertain significance (Dec 28, 2022)
4-83436961-T-C		not specified	Uncertain significance (Oct 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HELQ	protein_coding	protein_coding	ENST00000295488	18	48514

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.49e-12	0.998	125606	0	142	125748	0.000565

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	508	547	0.928	0.0000258	7189
Missense in Polyphen		115	134.05	0.85787		1724
Synonymous	0.174	198	201	0.984	0.00000983	2087
Loss of Function	2.87	26	47.3	0.549	0.00000219	691

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000574	0.000571
Ashkenazi Jewish	0.00102	0.000993
East Asian	0.000272	0.000272
Finnish	0.000188	0.000185
European (Non-Finnish)	0.000751	0.000739
Middle Eastern	0.000272	0.000272
South Asian	0.000717	0.000686
Other	0.000351	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Single-stranded DNA-dependent ATPase and 5' to 3' DNA helicase (PubMed:11751861). Involved in the repair of DNA cross- links and double-strand break (DSB) resistance. Participates in FANCD2-mediated repair. Forms a complex with POLN polymerase that participates in homologous recombination (HR) repair and is essential for cellular protection against DNA cross-links (PubMed:19995904). {ECO:0000269|PubMed:11751861, ECO:0000269|PubMed:19995904}.

Intolerance Scores

• rvis_EVS: 1.78
• rvis_percentile_EVS: 96.86

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.294
• ghis: 0.457

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Helq
• Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype; neoplasm

Gene ontology

• Biological process: double-strand break repair via homologous recombination
• Molecular function: DNA binding;helicase activity;protein binding;ATP binding