ZIK1

zinc finger protein interacting with K protein 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 19:57578456-57593890

Links

ENSG00000171649 ∙ NCBI:284307 ∙ ∙ HGNC:33104 ∙ Uniprot:Q3SY52 ∙ 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 ZIK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZIK1 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			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	1	0

Variants in ZIK1

This is a list of pathogenic ClinVar variants found in the ZIK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57578676-G-A		not specified	Uncertain significance (Jun 22, 2021)
19-57584369-G-A		not specified	Uncertain significance (Jun 29, 2023)
19-57584978-G-A		not specified	Uncertain significance (Apr 08, 2024)
19-57584979-G-T		not specified	Uncertain significance (Apr 08, 2024)
19-57588563-G-A		not specified	Uncertain significance (Aug 30, 2021)
19-57588651-T-C		not specified	Uncertain significance (Oct 05, 2023)
19-57590021-T-A		not specified	Uncertain significance (Nov 21, 2023)
19-57590040-A-C		not specified	Uncertain significance (Oct 12, 2022)
19-57590053-A-G		not specified	Uncertain significance (Oct 13, 2023)
19-57590115-T-G		not specified	Uncertain significance (Sep 26, 2023)
19-57590120-G-C		not specified	Uncertain significance (Jul 14, 2023)
19-57590163-C-G		not specified	Uncertain significance (Apr 20, 2024)
19-57590287-T-C		not specified	Uncertain significance (Jan 31, 2023)
19-57590314-G-A		not specified	Uncertain significance (Dec 06, 2021)
19-57590325-G-T		not specified	Uncertain significance (Jun 24, 2022)
19-57590352-C-T		not specified	Uncertain significance (Dec 15, 2023)
19-57590392-C-G		not specified	Uncertain significance (Aug 21, 2023)
19-57590422-T-A		not specified	Uncertain significance (Dec 20, 2023)
19-57590505-G-T		not specified	Uncertain significance (Aug 30, 2022)
19-57590532-T-C		not specified	Uncertain significance (Jan 24, 2024)
19-57590551-C-T		not specified	Uncertain significance (Dec 14, 2021)
19-57590553-T-G		not specified	Uncertain significance (Oct 10, 2023)
19-57590602-A-G		not specified	Uncertain significance (Jun 09, 2022)
19-57590607-C-G		not specified	Uncertain significance (May 30, 2023)
19-57590682-G-A		not specified	Uncertain significance (Dec 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZIK1	protein_coding	protein_coding	ENST00000597850	4	15322

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000276	0.190	125721	0	14	125735	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.525	232	256	0.908	0.0000125	3219
Missense in Polyphen		64	90.921	0.7039		1168
Synonymous	0.337	86	90.1	0.955	0.00000424	895
Loss of Function	-0.721	6	4.37	1.37	1.86e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000694	0.000677
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000280	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be a transcriptional repressor. {ECO:0000250}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• loftool: 0.853
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.0458
• hipred: N
• hipred_score: 0.112
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.244

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zik1

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding