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.

• not_specified (165 variants)

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. These statistics are base on transcript: NM_001012981.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			152	13		165
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	152	13	0

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