ZKSCAN3

zinc finger with KRAB and SCAN domains 3, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 6:28349947-28369172

Previous symbols: [ "ZNF306", "ZNF309" ]

Links

ENSG00000189298 ∙ NCBI:80317 ∙ OMIM:612791 ∙ HGNC:13853 ∙ Uniprot:Q9BRR0 ∙ 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 ZKSCAN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZKSCAN3 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in ZKSCAN3

This is a list of pathogenic ClinVar variants found in the ZKSCAN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28359683-G-T		not specified	Uncertain significance (Sep 26, 2022)
6-28359753-A-G		not specified	Uncertain significance (Aug 17, 2021)
6-28359822-T-G		not specified	Uncertain significance (Aug 02, 2021)
6-28359831-A-G		not specified	Uncertain significance (Oct 10, 2023)
6-28359926-G-T		not specified	Uncertain significance (Sep 13, 2023)
6-28361370-C-T		not specified	Uncertain significance (Aug 01, 2022)
6-28363359-G-A		not specified	Uncertain significance (Mar 07, 2024)
6-28363723-C-T		not specified	Uncertain significance (Jan 06, 2023)
6-28363762-G-T		not specified	Likely benign (Aug 15, 2023)
6-28365458-C-T		not specified	Uncertain significance (Sep 14, 2022)
6-28365551-G-A		not specified	Uncertain significance (Dec 19, 2023)
6-28365639-C-T		not specified	Uncertain significance (Jul 22, 2022)
6-28365663-A-G		not specified	Uncertain significance (Nov 03, 2023)
6-28365690-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-28365706-G-T			Uncertain significance (-)
6-28365720-T-C		not specified	Uncertain significance (Nov 30, 2022)
6-28365722-A-C		not specified	Uncertain significance (Dec 12, 2023)
6-28365737-C-T		not specified	Uncertain significance (Dec 27, 2022)
6-28365747-A-G		not specified	Uncertain significance (Jan 18, 2022)
6-28365846-C-A		not specified	Uncertain significance (Mar 21, 2023)
6-28365861-A-G		not specified	Uncertain significance (Jan 23, 2024)
6-28365891-G-C		not specified	Uncertain significance (Mar 07, 2024)
6-28365902-A-G		not specified	Uncertain significance (Nov 14, 2023)
6-28366226-A-G		not specified	Uncertain significance (Jul 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZKSCAN3	protein_coding	protein_coding	ENST00000377255	5	19257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-11	0.225	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.64	212	291	0.730	0.0000151	3539
Missense in Polyphen		70	94.945	0.73727		1174
Synonymous	1.11	100	115	0.869	0.00000621	1012
Loss of Function	0.844	19	23.4	0.812	0.00000136	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000756	0.000756
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.00	0.00
South Asian	0.000425	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional factor that binds to the consensus sequence 5'-[GT][AG][AGT]GGGG-3' and acts as a repressor of autophagy. Specifically represses expression of genes involved in autophagy and lysosome biogenesis/function such as MAP1LC3B, ULK1 or WIPI2. Associates with chromatin at the ITGB4 and VEGF promoters. Also acts as a transcription activator and promotes cancer cell progression and/or migration in various tumors and myelomas. {ECO:0000269|PubMed:18940803, ECO:0000269|PubMed:21057542, ECO:0000269|PubMed:22531714, ECO:0000269|PubMed:23434374}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.667
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.1

Haploinsufficiency Scores

• pHI: 0.160
• hipred: N
• hipred_score: 0.218
• ghis: 0.471

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.629

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zkscan3

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;autophagy;lysosome organization;negative regulation of autophagy;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;negative regulation of cellular senescence
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;metal ion binding