ZSCAN4

zinc finger and SCAN domain containing 4, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 19:57668934-57679152

Previous symbols: [ "ZNF494" ]

Links

ENSG00000180532 ∙ NCBI:201516 ∙ OMIM:613419 ∙ HGNC:23709 ∙ Uniprot:Q8NAM6 ∙ 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 ZSCAN4 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN4 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			10		1	11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	1

Variants in ZSCAN4

This is a list of pathogenic ClinVar variants found in the ZSCAN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-57676158-C-A		not specified	Uncertain significance (Mar 22, 2022)
19-57676168-T-C		not specified	Uncertain significance (Jul 09, 2021)
19-57676216-C-T		not specified	Uncertain significance (Jul 09, 2021)
19-57676348-T-C		not specified	Uncertain significance (Jan 27, 2022)
19-57676522-G-A		not specified	Uncertain significance (Sep 25, 2023)
19-57677974-G-A		not specified	Uncertain significance (Dec 26, 2023)
19-57678177-G-A		not specified	Likely benign (Jan 11, 2023)
19-57678180-C-G		not specified	Likely benign (Jan 29, 2024)
19-57678202-C-T		not specified	Likely benign (Jan 17, 2024)
19-57678261-A-G		not specified	Uncertain significance (Nov 09, 2023)
19-57678282-G-A		not specified	Uncertain significance (Dec 06, 2022)
19-57678282-G-C		not specified	Uncertain significance (Sep 14, 2022)
19-57678339-G-C		not specified	Uncertain significance (Oct 26, 2022)
19-57678391-T-C		not specified	Uncertain significance (Sep 30, 2021)
19-57678455-G-C			Benign (Dec 31, 2019)
19-57678754-G-A		not specified	Uncertain significance (Nov 15, 2021)
19-57678762-G-C		not specified	Uncertain significance (Dec 13, 2022)
19-57678846-A-G		not specified	Uncertain significance (Jan 09, 2024)
19-57678855-C-T		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN4	protein_coding	protein_coding	ENST00000318203	3	10218

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000433	0.418	110969	0	2	110971	0.00000901

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.439	209	228	0.918	0.0000109	2857
Missense in Polyphen		36	51.519	0.69878		709
Synonymous	-0.403	87	82.3	1.06	0.00000400	801
Loss of Function	0.292	7	7.89	0.888	3.30e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000324	0.0000324
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000189	0.000189

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Embryonic stem (ES) cell-specific transcription factor required to regulate ES cell pluripotency. Binds telomeres and plays a key role in genomic stability in ES cells by regulating telomere elongation. Acts as an activator of spontaneous telomere sister chromatid exchange (T-SCE) and telomere elongation in undifferentiated ES cells (By similarity). {ECO:0000250}.
• Pathway: Preimplantation Embryo (Consensus)

Recessive Scores

• pRec: 0.0716

Intolerance Scores

• loftool: 0.678
• rvis_EVS: -0.31
• rvis_percentile_EVS: 31.93

Haploinsufficiency Scores

• pHI: 0.0520
• hipred: N
• hipred_score: 0.123
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000169

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;telomere maintenance via telomere lengthening;negative regulation of mitotic recombination
• Cellular component: nuclear chromosome, telomeric region;nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding