ZKSCAN2

zinc finger with KRAB and SCAN domains 2, the group of Myb/SANT domain containing|SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 16:25236001-25257845

Previous symbols: [ "ZNF694" ]

Links

ENSG00000155592 ∙ NCBI:342357 ∙ ∙ HGNC:25677 ∙ Uniprot:Q63HK3 ∙ 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 ZKSCAN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN2 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			96	8		104
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	96	8	0

Variants in ZKSCAN2

This is a list of pathogenic ClinVar variants found in the ZKSCAN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-25239851-T-C		not specified	Uncertain significance (Nov 05, 2021)
16-25239889-G-A		not specified	Uncertain significance (May 08, 2024)
16-25239917-C-T		not specified	Uncertain significance (Jun 02, 2023)
16-25239952-C-T		not specified	Uncertain significance (Aug 02, 2021)
16-25239961-C-T		not specified	Uncertain significance (Aug 01, 2022)
16-25239979-G-A		not specified	Uncertain significance (Dec 31, 2024)
16-25240003-C-T		not specified	Uncertain significance (Sep 26, 2023)
16-25240012-C-T		not specified	Uncertain significance (Apr 22, 2024)
16-25240060-T-C		not specified	Uncertain significance (Oct 27, 2023)
16-25240072-C-A		not specified	Uncertain significance (Feb 06, 2025)
16-25240087-C-T		not specified	Uncertain significance (Sep 16, 2021)
16-25240107-A-C		not specified	Uncertain significance (Feb 21, 2025)
16-25240180-A-G		not specified	Uncertain significance (Jul 28, 2021)
16-25240181-T-G		not specified	Uncertain significance (Dec 19, 2023)
16-25240183-A-G		not specified	Uncertain significance (Jul 26, 2022)
16-25240220-C-T		not specified	Uncertain significance (Aug 16, 2022)
16-25240250-T-G		not specified	Uncertain significance (Mar 02, 2023)
16-25240288-C-G		not specified	Uncertain significance (Oct 11, 2024)
16-25240322-C-T		not specified	Uncertain significance (Jul 30, 2024)
16-25240336-C-A		not specified	Uncertain significance (Dec 17, 2023)
16-25240366-C-A		not specified	Uncertain significance (Jul 13, 2021)
16-25240394-T-G		not specified	Uncertain significance (Jan 03, 2022)
16-25240403-T-A		not specified	Uncertain significance (Jan 22, 2025)
16-25240424-G-C		not specified	Uncertain significance (Dec 08, 2023)
16-25240435-C-T		not specified	Uncertain significance (Apr 07, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZKSCAN2	protein_coding	protein_coding	ENST00000328086	7	21931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000284	1.00	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.249	528	544	0.970	0.0000310	6371
Missense in Polyphen		153	184.5	0.82928		2284
Synonymous	-0.902	209	193	1.08	0.0000105	1834
Loss of Function	3.92	16	44.1	0.363	0.00000273	491

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000271	0.000271
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000185	0.000185
Middle Eastern	0.000109	0.000109
South Asian	0.000294	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation.

Intolerance Scores

• loftool: 0.690
• rvis_EVS: 0.34
• rvis_percentile_EVS: 73.74

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.376
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.110

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan2

Gene ontology

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