HELZ

protein-coding

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

Gene summary

HELZ is a member of the superfamily I class of RNA helicases. RNA helicases alter the conformation of RNA by unwinding double-stranded regions, thereby altering the biologic activity of the RNA molecule and regulating access to other proteins (Wagner et al., 1999 [PubMed 10471385]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_014877.4

Inheritance

—

ClinVar variants

P:1U:216B:10

Top phenotype

Abnormal brain morphology

gnomAD constraint

pLI —, LoF o/e 0.01

Max pathogenic AF

—

Genomic locus

chr17:67,070,444-67,245,989

External References & Databases

Ensembl (ENSG00000198265)

Transcript & Mutation Effects

hg38 • Region Span ~175.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HELZ variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 204

not providedTotal: 4

Abnormal brain morphologyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014877.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense		1 clinvar	207 clinvar	9 clinvar		217
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	1	216	10	0	227

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014877.4	RefSeq	NP_055692.3	30	MANE Select
ENST00000358691.10	Ensembl	ENSP00000351524.5	30	MANE Select
NM_001330447.2	RefSeq	NP_001317376.2	30	Standard
ENST00000417253.7	Ensembl	ENSP00000411144.3	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

posttranscriptional gene silencing by RNA

Molecular Function

RNA binding
helicase activity
protein binding
ATP binding
metal ion binding

Cellular Component

nucleus
cytosol
membrane
P granule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358691
Coding exons: 30
Length: 175552
Individuals with no LoFs: 124780
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 124784
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.30	747	1.05e+3	0.713	0.0000548	12723
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000027	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.851

Gene Damage Prediction

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