ZSCAN23

zinc finger and SCAN domain containing 23, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 6:28431930-28443502

Previous symbols: [ "ZNF453", "ZNF390" ]

Links

ENSG00000187987 ∙ NCBI:222696 ∙ ∙ HGNC:21193 ∙ Uniprot:Q3MJ62 ∙ 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 ZSCAN23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN23 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			17	3		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	3	0

Variants in ZSCAN23

This is a list of pathogenic ClinVar variants found in the ZSCAN23 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28434469-C-T		not specified	Uncertain significance (Jun 30, 2022)
6-28434484-G-A		not specified	Uncertain significance (Jul 26, 2023)
6-28434496-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-28434560-T-C		not specified	Uncertain significance (Jun 18, 2024)
6-28434576-T-A		not specified	Uncertain significance (Jul 10, 2024)
6-28434652-G-T		not specified	Uncertain significance (May 10, 2024)
6-28434713-T-A		not specified	Uncertain significance (Jan 03, 2024)
6-28434784-C-T		not specified	Uncertain significance (Aug 21, 2024)
6-28434796-T-G		not specified	Uncertain significance (Mar 28, 2023)
6-28434809-G-C		not specified	Uncertain significance (May 05, 2023)
6-28434831-C-G		not specified	Uncertain significance (Jan 22, 2024)
6-28434839-C-T		not specified	Uncertain significance (Dec 19, 2023)
6-28434853-T-C		not specified	Uncertain significance (Dec 15, 2022)
6-28434889-T-C		not specified	Uncertain significance (Aug 28, 2023)
6-28434895-C-T		not specified	Uncertain significance (Jun 21, 2022)
6-28434925-T-C		not specified	Uncertain significance (Nov 24, 2024)
6-28434940-C-T		not specified	Likely benign (Dec 07, 2022)
6-28434977-T-C		not specified	Uncertain significance (Dec 01, 2022)
6-28434988-T-A		not specified	Likely benign (May 04, 2022)
6-28435508-C-G		not specified	Uncertain significance (Apr 18, 2023)
6-28435570-T-G		not specified	Uncertain significance (Nov 06, 2023)
6-28435932-C-T		not specified	Likely benign (Dec 19, 2022)
6-28435972-T-G		not specified	Uncertain significance (May 24, 2024)
6-28436031-G-C		not specified	Uncertain significance (Jan 19, 2024)
6-28436080-G-A		not specified	Uncertain significance (Mar 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN23	protein_coding	protein_coding	ENST00000289788	3	11573

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.11e-10	0.104	125635	0	21	125656	0.0000836

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.48	144	203	0.708	0.0000104	2543
Missense in Polyphen		36	67.225	0.53552		827
Synonymous	1.65	55	73.0	0.754	0.00000330	722
Loss of Function	0.223	15	16.0	0.940	8.20e-7	197

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000163	0.000162
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000115	0.000106
Middle Eastern	0.00	0.00
South Asian	0.0000349	0.0000327
Other	0.000524	0.000489

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.135
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.302

Gene Damage Prediction

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

Gene ontology

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