ZSCAN20

zinc finger and SCAN domain containing 20, the group of Zinc fingers C2H2-type|Myb/SANT domain containing|SCAN domain containing

Basic information

Region (hg38): 1:33472645-33501643

Previous symbols: [ "ZNF360", "ZNF31" ]

Links

ENSG00000121903 ∙ NCBI:7579 ∙ OMIM:611315 ∙ HGNC:13093 ∙ Uniprot:P17040 ∙ 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 ZSCAN20 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN20 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			43	3		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	43	3	0

Variants in ZSCAN20

This is a list of pathogenic ClinVar variants found in the ZSCAN20 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-33479299-C-G		not specified	Uncertain significance (Jul 13, 2022)
1-33479397-T-C		not specified	Likely benign (Apr 05, 2023)
1-33479437-C-G		not specified	Uncertain significance (Mar 01, 2024)
1-33479471-T-G		not specified	Uncertain significance (Apr 04, 2024)
1-33479542-G-A		not specified	Uncertain significance (Dec 01, 2022)
1-33479550-G-A		not specified	Uncertain significance (Sep 17, 2021)
1-33479551-A-T		not specified	Uncertain significance (Sep 17, 2021)
1-33479601-A-G		not specified	Uncertain significance (Oct 25, 2023)
1-33479658-G-A		not specified	Uncertain significance (Sep 15, 2021)
1-33479694-G-T		not specified	Uncertain significance (Nov 10, 2021)
1-33488494-G-T		not specified	Uncertain significance (Sep 25, 2023)
1-33488567-C-A		not specified	Uncertain significance (May 04, 2022)
1-33488637-C-T		not specified	Uncertain significance (Mar 19, 2024)
1-33489570-C-T		not specified	Uncertain significance (Sep 15, 2021)
1-33489584-G-A		not specified	Uncertain significance (Apr 06, 2023)
1-33489590-A-T		not specified	Uncertain significance (Nov 29, 2021)
1-33489593-G-A		not specified	Uncertain significance (Dec 21, 2023)
1-33491069-G-A		not specified	Uncertain significance (Dec 07, 2021)
1-33491123-G-A		not specified	Uncertain significance (May 24, 2023)
1-33491202-A-T		not specified	Uncertain significance (May 30, 2024)
1-33491219-G-A		not specified	Uncertain significance (Nov 21, 2023)
1-33491265-C-A		not specified	Uncertain significance (May 20, 2024)
1-33491300-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-33491330-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-33491376-T-C		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN20	protein_coding	protein_coding	ENST00000361328	7	23862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000481	1.00	125183	0	34	125217	0.000136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	486	576	0.843	0.0000319	6877
Missense in Polyphen		149	228.69	0.65153		2645
Synonymous	0.425	207	215	0.963	0.0000114	1976
Loss of Function	4.08	14	42.9	0.327	0.00000216	514

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000290	0.000289
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.000165	0.000163
Finnish	0.0000464	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000165	0.000163
South Asian	0.000164	0.000163
Other	0.000165	0.000164

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0898

Intolerance Scores

• loftool: 0.578
• rvis_EVS: -0.53
• rvis_percentile_EVS: 20.91

Haploinsufficiency Scores

• pHI: 0.427
• hipred: N
• hipred_score: 0.304
• ghis: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.688

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan20

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