HELZ2

helicase with zinc finger 2, the group of UPF1 like RNA helicases

Basic information

Region (hg38): 20:63558086-63574239

Links

ENSG00000130589 ∙ NCBI:85441 ∙ OMIM:611265 ∙ HGNC:30021 ∙ Uniprot:Q9BYK8 ∙ 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 HELZ2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HELZ2 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				9	3	12
missense			228	34	3	265
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	228	43	6

Variants in HELZ2

This is a list of pathogenic ClinVar variants found in the HELZ2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-63559255-C-T		not specified	Uncertain significance (Jun 06, 2023)
20-63559278-G-A			Benign (Jul 11, 2017)
20-63559288-G-A			Likely benign (Mar 01, 2023)
20-63559297-G-A			Likely benign (Oct 01, 2022)
20-63559352-C-T		not specified	Uncertain significance (May 26, 2022)
20-63559957-G-A		not specified	Uncertain significance (Jan 23, 2024)
20-63559978-T-C		not specified	Uncertain significance (Mar 29, 2023)
20-63560029-C-T		not specified	Uncertain significance (Jun 26, 2023)
20-63560030-G-A		not specified	Uncertain significance (Sep 17, 2021)
20-63560059-C-T		not specified	Uncertain significance (Feb 03, 2022)
20-63560064-G-A			Likely benign (Jun 01, 2022)
20-63560083-C-T		not specified	Uncertain significance (Apr 28, 2022)
20-63560176-C-T		not specified	Uncertain significance (Mar 06, 2023)
20-63560216-C-G		not specified	Uncertain significance (Oct 12, 2022)
20-63560221-C-T		not specified	Uncertain significance (Feb 28, 2024)
20-63560222-G-A		not specified	Uncertain significance (Feb 07, 2023)
20-63560251-G-A		not specified	Uncertain significance (May 27, 2022)
20-63560270-C-T		not specified	Likely benign (Sep 15, 2021)
20-63560324-G-A		not specified	Uncertain significance (Nov 17, 2022)
20-63560496-C-T		not specified	Uncertain significance (Mar 02, 2023)
20-63560524-T-A		not specified	Uncertain significance (Oct 03, 2022)
20-63560549-C-T		not specified	Likely benign (May 06, 2024)
20-63560553-C-T		not specified	Uncertain significance (Dec 12, 2023)
20-63560601-C-T		not specified	Uncertain significance (Feb 07, 2023)
20-63560825-G-A			Likely benign (Jun 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HELZ2	protein_coding	protein_coding	ENST00000467148	19	16154

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.34e-8	1.00	125624	1	81	125706	0.000326

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.433	1684	1.73e+3	0.971	0.000130	16690
Missense in Polyphen		516	630.41	0.81851		6878
Synonymous	-0.580	817	796	1.03	0.0000632	5696
Loss of Function	5.75	31	89.8	0.345	0.00000430	942

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000573	0.000572
Ashkenazi Jewish	0.000369	0.000298
East Asian	0.000512	0.000489
Finnish	0.000104	0.0000924
European (Non-Finnish)	0.000323	0.000299
Middle Eastern	0.000512	0.000489
South Asian	0.000610	0.000555
Other	0.000528	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Helicase that acts as a transcriptional coactivator for a number of nuclear receptors including PPARA, PPARG, THRA, THRB and RXRA. {ECO:0000269|PubMed:16239304, ECO:0000269|PubMed:23525231}.
• Pathway: Developmental Biology;Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha);Metabolism of lipids;Metabolism;Transcriptional regulation of white adipocyte differentiation (Consensus)

Intolerance Scores

• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.270
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Helz2
• Phenotype: liver/biliary system phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: nuclear-transcribed mRNA catabolic process, nonsense-mediated decay;regulation of lipid metabolic process;positive regulation of transcription by RNA polymerase II;RNA phosphodiester bond hydrolysis
• Cellular component: nucleoplasm;cytoplasm;membrane
• Molecular function: DNA binding;RNA binding;ATP-dependent RNA helicase activity;ribonuclease activity;protein binding;ATP binding;nuclear receptor transcription coactivator activity;metal ion binding