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

ENSG00000155592NCBI:342357HGNC:25677Uniprot:Q63HK3AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
8
clinvar
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)2390154
16-25239889-G-A not specified Uncertain significance (May 08, 2024)3334747
16-25239917-C-T not specified Uncertain significance (Jun 02, 2023)2556217
16-25239952-C-T not specified Uncertain significance (Aug 02, 2021)2353638
16-25239961-C-T not specified Uncertain significance (Aug 01, 2022)2304273
16-25239979-G-A not specified Uncertain significance (Dec 31, 2024)3819468
16-25240003-C-T not specified Uncertain significance (Sep 26, 2023)3193647
16-25240012-C-T not specified Uncertain significance (Apr 22, 2024)3334746
16-25240060-T-C not specified Uncertain significance (Oct 27, 2023)3193646
16-25240072-C-A not specified Uncertain significance (Feb 06, 2025)3819477
16-25240087-C-T not specified Uncertain significance (Sep 16, 2021)2345982
16-25240107-A-C not specified Uncertain significance (Feb 21, 2025)3819482
16-25240180-A-G not specified Uncertain significance (Jul 28, 2021)2239871
16-25240181-T-G not specified Uncertain significance (Dec 19, 2023)3193645
16-25240183-A-G not specified Uncertain significance (Jul 26, 2022)2303589
16-25240220-C-T not specified Uncertain significance (Aug 16, 2022)2409065
16-25240250-T-G not specified Uncertain significance (Mar 02, 2023)2493191
16-25240288-C-G not specified Uncertain significance (Oct 11, 2024)3473879
16-25240322-C-T not specified Uncertain significance (Jul 30, 2024)3473881
16-25240336-C-A not specified Uncertain significance (Dec 17, 2023)3193644
16-25240366-C-A not specified Uncertain significance (Jul 13, 2021)3193643
16-25240394-T-G not specified Uncertain significance (Jan 03, 2022)2209371
16-25240403-T-A not specified Uncertain significance (Jan 22, 2025)3819476
16-25240424-G-C not specified Uncertain significance (Dec 08, 2023)3193642
16-25240435-C-T not specified Uncertain significance (Apr 07, 2022)2356763

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZKSCAN2protein_codingprotein_codingENST00000328086 721931
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00002841.001257040441257480.000175
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2495285440.9700.00003106371
Missense in Polyphen153184.50.829282284
Synonymous-0.9022091931.080.00001051834
Loss of Function3.921644.10.3630.00000273491

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002710.000271
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.0001850.000185
European (Non-Finnish)0.0001850.000185
Middle Eastern0.0001090.000109
South Asian0.0002940.000294
Other0.0003260.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Zkscan2
Phenotype

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