HELZ

helicase with zinc finger, the group of UPF1 like RNA helicases|Zinc fingers CCCH-type

Basic information

Region (hg38): 17:67070443-67245989

Links

ENSG00000198265 ∙ NCBI:9931 ∙ OMIM:606699 ∙ HGNC:16878 ∙ Uniprot:P42694 ∙ 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 HELZ gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HELZ 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				1		1
missense		1	76	2		79
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	76	3	0

Variants in HELZ

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

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

Position	Type	Phenotype	Significance	ClinVar
17-67078314-A-G		not specified	Uncertain significance (Oct 27, 2022)
17-67078418-G-A		not specified	Uncertain significance (Nov 09, 2021)
17-67078568-T-C		not specified	Uncertain significance (Jan 04, 2022)
17-67086889-G-C		not specified	Uncertain significance (Jun 23, 2023)
17-67086933-T-C		not specified	Uncertain significance (Mar 25, 2024)
17-67086946-G-T		not specified	Uncertain significance (Sep 23, 2023)
17-67087002-A-G		not specified	Likely benign (Feb 06, 2023)
17-67087059-C-T		not specified	Uncertain significance (Nov 22, 2021)
17-67107215-A-G		not specified	Uncertain significance (Sep 23, 2023)
17-67107219-G-A		not specified	Uncertain significance (Nov 09, 2023)
17-67107261-T-C		not specified	Uncertain significance (Dec 21, 2022)
17-67107405-G-C		not specified	Uncertain significance (Sep 07, 2022)
17-67107455-C-T		not specified	Uncertain significance (Sep 01, 2022)
17-67107483-C-G		not specified	Uncertain significance (Feb 22, 2023)
17-67107488-A-G		not specified	Uncertain significance (Feb 06, 2023)
17-67107507-T-G		not specified	Uncertain significance (May 25, 2022)
17-67107546-G-C		not specified	Uncertain significance (Aug 10, 2021)
17-67107555-G-A		not specified	Uncertain significance (Oct 17, 2023)
17-67107570-T-C		not specified	Uncertain significance (May 17, 2023)
17-67107635-C-T		not specified	Uncertain significance (Apr 08, 2023)
17-67107644-C-G		not specified	Uncertain significance (Aug 22, 2023)
17-67107656-T-C		not specified	Uncertain significance (Sep 25, 2023)
17-67107664-T-G		not specified	Uncertain significance (Mar 28, 2024)
17-67108558-G-A		not specified	Uncertain significance (Feb 14, 2024)
17-67108565-G-A		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HELZ	protein_coding	protein_coding	ENST00000358691	30	175552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.29e-16	124780	0	4	124784	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.30	747	1.05e+3	0.713	0.0000548	12723
Missense in Polyphen		115	283.85	0.40515		3446
Synonymous	0.235	371	377	0.985	0.0000201	3755
Loss of Function	9.10	1	98.5	0.0102	0.00000513	1148

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000270	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a helicase that plays a role in RNA metabolism in multiple tissues and organs within the developing embryo.

Recessive Scores

• pRec: 0.0983

Intolerance Scores

• loftool: 0.00468
• rvis_EVS: -1.21
• rvis_percentile_EVS: 5.71

Haploinsufficiency Scores

• pHI: 0.336
• hipred: Y
• hipred_score: 0.673
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Helz
• Phenotype: normal phenotype

Gene ontology

• Biological process: posttranscriptional gene silencing by RNA
• Cellular component: nucleus;cytosol;membrane;P granule
• Molecular function: RNA binding;helicase activity;protein binding;ATP binding;metal ion binding