ANKZF1

ankyrin repeat and zinc finger peptidyl tRNA hydrolase 1, the group of Zinc fingers C2H2-type|Ankyrin repeat domain containing

Basic information

Region (hg38): 2:219229783-219236679

Links

ENSG00000163516 ∙ NCBI:55139 ∙ OMIM:617541 ∙ HGNC:25527 ∙ Uniprot:Q9H8Y5 ∙ 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 ANKZF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ANKZF1 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			2	86	5	93
missense			293	6	11	310
nonsense			21			21
start loss			1			1
frameshift			24			24
inframe indel			10	2	1	13
splice donor/acceptor (+/-2bp)			6			6
splice region			11	7	1	19
non coding			20	56	4	80
Total	0	0	377	150	21

Variants in ANKZF1

This is a list of pathogenic ClinVar variants found in the ANKZF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-219230258-A-G			Uncertain significance (Mar 03, 2024)
2-219230263-G-A			Likely benign (Jan 23, 2025)
2-219230266-G-C			Likely benign (May 27, 2022)
2-219230267-G-T			Uncertain significance (Sep 11, 2023)
2-219230271-C-T			Uncertain significance (Jan 12, 2022)
2-219230273-G-C		not specified	Uncertain significance (May 16, 2024)
2-219230279-G-T			Uncertain significance (Jul 08, 2024)
2-219230279-G-GC			Uncertain significance (Oct 24, 2023)
2-219230288-C-T			Uncertain significance (Mar 01, 2024)
2-219230298-T-A			Uncertain significance (May 04, 2022)
2-219230302-CCT-C			Uncertain significance (May 02, 2024)
2-219230308-T-G		not specified	Uncertain significance (Aug 17, 2022)
2-219230311-C-T			Likely benign (Nov 17, 2023)
2-219230315-A-G			Uncertain significance (Aug 17, 2023)
2-219230316-G-A			Uncertain significance (Jul 14, 2022)
2-219230327-C-G		not specified	Uncertain significance (Dec 31, 2024)
2-219230328-C-T			Uncertain significance (Sep 08, 2022)
2-219230330-G-A		not specified	Conflicting classifications of pathogenicity (Nov 28, 2023)
2-219230336-C-G			Likely benign (Jan 21, 2025)
2-219230340-G-T			Uncertain significance (Dec 10, 2024)
2-219230342-C-T			Likely benign (Oct 21, 2024)
2-219230343-TGAGCCTGGTGAGCCAC-T			Uncertain significance (Dec 30, 2021)
2-219230351-G-C			Uncertain significance (Nov 28, 2022)
2-219230375-C-CT			Uncertain significance (Aug 12, 2024)
2-219230380-C-T			Likely benign (Oct 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ANKZF1	protein_coding	protein_coding	ENST00000323348	13	6913

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.82e-26	0.000654	124797	0	218	125015	0.000872

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.243	447	433	1.03	0.0000264	4615
Missense in Polyphen		118	114.8	1.0279		1204
Synonymous	-0.318	167	162	1.03	0.00000805	1556
Loss of Function	0.310	40	42.2	0.949	0.00000282	410

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00133	0.00133
Ashkenazi Jewish	0.000511	0.000497
East Asian	0.00207	0.00204
Finnish	0.000190	0.000185
European (Non-Finnish)	0.000507	0.000503
Middle Eastern	0.00207	0.00204
South Asian	0.00263	0.00252
Other	0.000671	0.000658

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the cellular response to hydrogen peroxide and in the maintenance of mitochondrial integrity under conditions of cellular stress (PubMed:28302725). Involved in the endoplasmic reticulum (ER)-associated degradation (ERAD) pathway (By similarity). {ECO:0000250, ECO:0000269|PubMed:28302725}.

Recessive Scores

• pRec: 0.0747

Intolerance Scores

• loftool: 0.692
• rvis_EVS: 0.61
• rvis_percentile_EVS: 82.93

Haploinsufficiency Scores

• pHI: 0.323
• hipred: N
• hipred_score: 0.311
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ankzf1

Gene ontology

• Biological process: ubiquitin-dependent ERAD pathway;cellular response to hydrogen peroxide;nuclear protein quality control by the ubiquitin-proteasome system;mitochondria-associated ubiquitin-dependent protein catabolic process
• Cellular component: cytoplasm;membrane;Cdc48p-Npl4p-Vms1p AAA ATPase complex
• Molecular function: nucleic acid binding;thiol-dependent ubiquitin-specific protease activity;protein binding;metal ion binding