ZKSCAN1

zinc finger with KRAB and SCAN domains 1, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 7:100015571-100041689

Previous symbols: [ "ZNF139", "ZNF36" ]

Links

ENSG00000106261 ∙ NCBI:7586 ∙ OMIM:601260 ∙ HGNC:13101 ∙ Uniprot:P17029 ∙ 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 ZKSCAN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN1 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	1	0

Variants in ZKSCAN1

This is a list of pathogenic ClinVar variants found in the ZKSCAN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100023535-C-T		not specified	Uncertain significance (Oct 04, 2022)
7-100023596-G-C		not specified	Uncertain significance (Dec 09, 2023)
7-100023665-G-C		not specified	Uncertain significance (Jul 07, 2022)
7-100023687-C-T		not specified	Uncertain significance (Jun 22, 2021)
7-100023688-G-T		not specified	Uncertain significance (Nov 22, 2022)
7-100023718-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-100023754-A-G		not specified	Uncertain significance (Oct 27, 2021)
7-100023762-C-T		not specified	Uncertain significance (Oct 27, 2023)
7-100023763-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-100023837-G-A		not specified	Uncertain significance (Feb 15, 2023)
7-100023886-C-T		not specified	Uncertain significance (Oct 05, 2021)
7-100024187-G-A		not specified	Uncertain significance (Oct 03, 2022)
7-100024247-G-A		not specified	Uncertain significance (Dec 19, 2022)
7-100024272-A-G		not specified	Uncertain significance (Feb 02, 2024)
7-100024275-C-T		not specified	Uncertain significance (Nov 21, 2023)
7-100024290-G-A		not specified	Uncertain significance (Apr 07, 2022)
7-100024305-G-A		not specified	Uncertain significance (Aug 17, 2021)
7-100029861-C-G		not specified	Uncertain significance (Jun 19, 2024)
7-100029887-C-T		not specified	Uncertain significance (Nov 18, 2022)
7-100029894-A-C		not specified	Uncertain significance (Jan 29, 2024)
7-100029911-G-C		not specified	Uncertain significance (Dec 06, 2023)
7-100029938-A-G		not specified	Uncertain significance (May 10, 2024)
7-100029943-G-A			Likely benign (Apr 01, 2023)
7-100030270-A-G		not specified	Uncertain significance (Sep 16, 2021)
7-100033319-A-G		not specified	Uncertain significance (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZKSCAN1	protein_coding	protein_coding	ENST00000324306	5	26109

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.969	0.0306	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	224	333	0.673	0.0000192	3703
Missense in Polyphen		65	140.25	0.46346		1629
Synonymous	0.513	120	127	0.942	0.00000753	1084
Loss of Function	3.97	3	24.0	0.125	0.00000135	279

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.498
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.5

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.496
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.830

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan1

Gene ontology

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