ZKSCAN5

zinc finger with KRAB and SCAN domains 5, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 7:99504662-99534700

Previous symbols: [ "ZFP95" ]

Links

ENSG00000196652 ∙ NCBI:23660 ∙ OMIM:611272 ∙ HGNC:12867 ∙ Uniprot:Q9Y2L8 ∙ 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 ZKSCAN5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN5 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			34	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	34	1	1

Variants in ZKSCAN5

This is a list of pathogenic ClinVar variants found in the ZKSCAN5 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99506085-C-T		not specified	Uncertain significance (Jun 07, 2024)
7-99506087-C-T		not specified	Uncertain significance (Mar 28, 2024)
7-99506100-C-A		not specified	Uncertain significance (Jul 12, 2022)
7-99506177-A-T		not specified	Uncertain significance (Aug 05, 2024)
7-99506181-T-C		not specified	Uncertain significance (Aug 10, 2021)
7-99506209-C-G		not specified	Uncertain significance (Aug 28, 2024)
7-99506219-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-99506397-G-T		not specified	Uncertain significance (Apr 15, 2024)
7-99506426-A-G		not specified	Uncertain significance (Aug 04, 2021)
7-99506457-A-G		not specified	Uncertain significance (Jul 05, 2022)
7-99512472-T-C		not specified	Uncertain significance (May 24, 2023)
7-99512482-G-A			Benign (Dec 31, 2019)
7-99512567-A-G		not specified	Uncertain significance (Feb 13, 2024)
7-99512571-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-99512574-G-A		not specified	Likely benign (Sep 29, 2022)
7-99512590-T-C			Benign (Jun 26, 2018)
7-99520197-A-C		not specified	Uncertain significance (Aug 03, 2022)
7-99520242-A-T		not specified	Uncertain significance (Mar 01, 2023)
7-99525816-A-G		not specified	Uncertain significance (Mar 13, 2023)
7-99525878-T-C		not specified	Uncertain significance (Jan 08, 2024)
7-99525885-C-T		not specified	Uncertain significance (Oct 19, 2024)
7-99525888-C-T		not specified	Uncertain significance (Feb 14, 2024)
7-99525915-A-G		not specified	Uncertain significance (Aug 02, 2024)
7-99525917-G-A		not specified	Uncertain significance (Dec 14, 2022)
7-99525944-C-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZKSCAN5	protein_coding	protein_coding	ENST00000394170	6	30050

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0876	0.912	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.42	374	460	0.813	0.0000258	5604
Missense in Polyphen		114	181.29	0.62884		2133
Synonymous	-0.147	175	173	1.01	0.00000992	1527
Loss of Function	4.07	9	35.0	0.257	0.00000183	423

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000423	0.000423
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000327	0.000326
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000195	0.000185
Middle Eastern	0.000327	0.000326
South Asian	0.0000980	0.0000980
Other	0.000189	0.000163

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: 0.0926

Intolerance Scores

• loftool: 0.801
• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.67

Haploinsufficiency Scores

• pHI: 0.384
• hipred: N
• hipred_score: 0.372
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan5

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;zinc ion binding