ZKSCAN4

zinc finger with KRAB and SCAN domains 4, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 6:28241697-28252269

Previous symbols: [ "ZNF307", "ZNF427" ]

Links

ENSG00000187626 ∙ NCBI:387032 ∙ OMIM:611643 ∙ HGNC:13854 ∙ Uniprot:Q969J2 ∙ 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 ZKSCAN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN4 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		2
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	3	0

Variants in ZKSCAN4

This is a list of pathogenic ClinVar variants found in the ZKSCAN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28245132-T-G		not specified	Uncertain significance (Jun 19, 2024)
6-28245172-A-G		not specified	Uncertain significance (May 16, 2022)
6-28245177-C-T		not specified	Uncertain significance (Nov 20, 2023)
6-28245208-G-C		not specified	Uncertain significance (Mar 07, 2024)
6-28245291-T-G		not specified	Uncertain significance (Apr 25, 2022)
6-28245297-G-T		not specified	Uncertain significance (May 13, 2024)
6-28245405-T-A		not specified	Uncertain significance (Apr 14, 2022)
6-28245446-C-T		not specified	Uncertain significance (Jan 03, 2022)
6-28245615-T-G		not specified	Uncertain significance (Oct 06, 2021)
6-28245616-C-T		not specified	Uncertain significance (May 04, 2023)
6-28245639-C-T		not specified	Uncertain significance (Jan 10, 2023)
6-28245657-T-A		not specified	Uncertain significance (Dec 02, 2022)
6-28245765-G-A		not specified	Uncertain significance (Jan 09, 2024)
6-28245827-T-G		not specified	Uncertain significance (Apr 13, 2022)
6-28245880-C-T		not specified	Uncertain significance (May 16, 2023)
6-28247070-A-C		not specified	Uncertain significance (May 01, 2022)
6-28248075-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-28248114-A-G		not specified	Uncertain significance (Feb 28, 2023)
6-28248138-G-C		not specified	Uncertain significance (Jul 06, 2021)
6-28249694-G-T		not specified	Likely benign (Jan 23, 2024)
6-28249695-T-C		not specified	Uncertain significance (Jan 26, 2023)
6-28249737-T-C		not specified	Uncertain significance (May 06, 2024)
6-28249828-C-T		not specified	Uncertain significance (Jun 24, 2022)
6-28251568-G-C		not specified	Uncertain significance (May 14, 2024)
6-28251599-A-G			Likely benign (May 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZKSCAN4	protein_coding	protein_coding	ENST00000377294	5	14611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000142	0.993	125631	1	116	125748	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.07	238	289	0.822	0.0000137	3580
Missense in Polyphen		67	100.81	0.66461		1299
Synonymous	1.30	97	115	0.845	0.00000569	1033
Loss of Function	2.37	10	22.0	0.455	0.00000104	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000405	0.000405
Ashkenazi Jewish	0.00	0.00
East Asian	0.00120	0.00114
Finnish	0.00250	0.00250
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.00120	0.00114
South Asian	0.0000653	0.0000653
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the transcriptional activation of MDM2 and EP300 genes. {ECO:0000269|PubMed:17910948}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• loftool: 0.902
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.7

Haploinsufficiency Scores

• pHI: 0.104
• hipred: N
• hipred_score: 0.218
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.891

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan4

Gene ontology

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