ZKSCAN7

zinc finger with KRAB and SCAN domains 7, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 3:44555193-44594173

Previous symbols: [ "ZNF64", "ZNF448", "ZNF167" ]

Links

ENSG00000196345 ∙ NCBI:55888 ∙ ∙ HGNC:12955 ∙ Uniprot:Q9P0L1 ∙ 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 ZKSCAN7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN7 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			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	4	0

Variants in ZKSCAN7

This is a list of pathogenic ClinVar variants found in the ZKSCAN7 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-44557081-A-G		not specified	Uncertain significance (Mar 22, 2023)
3-44557091-G-A		not specified	Uncertain significance (May 20, 2024)
3-44557168-A-C		not specified	Uncertain significance (May 01, 2024)
3-44557175-A-T		not specified	Uncertain significance (Mar 29, 2024)
3-44557192-G-A		not specified	Uncertain significance (Feb 05, 2024)
3-44557241-T-C		not specified	Uncertain significance (Oct 10, 2023)
3-44557286-G-A		not specified	Likely benign (Apr 05, 2023)
3-44557396-C-T		not specified	Uncertain significance (Jan 08, 2024)
3-44565590-C-G		not specified	Uncertain significance (Dec 15, 2023)
3-44567986-C-T		not specified	Uncertain significance (Nov 30, 2021)
3-44567998-C-T		not specified	Uncertain significance (Apr 25, 2022)
3-44568311-C-T		not specified	Uncertain significance (Aug 17, 2021)
3-44568316-G-A		not specified	Uncertain significance (Jan 24, 2023)
3-44568335-T-A		not specified	Uncertain significance (Mar 16, 2022)
3-44568361-A-G		not specified	Likely benign (May 21, 2024)
3-44568367-A-G		not specified	Likely benign (May 24, 2024)
3-44568379-A-G		not specified	Uncertain significance (Dec 13, 2021)
3-44570018-G-A		not specified	Uncertain significance (Sep 06, 2022)
3-44570050-G-A		not specified	Uncertain significance (Apr 23, 2024)
3-44570066-T-C		not specified	Likely benign (Aug 30, 2021)
3-44570087-C-G		not specified	Uncertain significance (Dec 18, 2023)
3-44570102-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-44570175-C-G		not specified	Likely benign (May 08, 2024)
3-44570176-A-G		not specified	Likely benign (May 08, 2024)
3-44570224-G-A		not specified	Uncertain significance (Feb 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZKSCAN7	protein_coding	protein_coding	ENST00000273320	5	28291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000134	0.998	125579	0	169	125748	0.000672

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.146	381	389	0.979	0.0000198	4968
Missense in Polyphen		125	135.66	0.9214		1804
Synonymous	-1.46	163	141	1.16	0.00000677	1412
Loss of Function	2.74	13	28.9	0.450	0.00000170	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00139	0.00139
Ashkenazi Jewish	0.00467	0.00467
East Asian	0.000222	0.000217
Finnish	0.000601	0.000601
European (Non-Finnish)	0.000593	0.000589
Middle Eastern	0.000222	0.000217
South Asian	0.000163	0.000163
Other	0.000490	0.000489

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: 0.279

Intolerance Scores

• rvis_EVS: 0.94
• rvis_percentile_EVS: 89.86

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.132
• ghis: 0.521

Essentials

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

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan7

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;protein binding;metal ion binding