ZSCAN1

zinc finger and SCAN domain containing 1, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 19:58034024-58054631

Links

ENSG00000152467 ∙ NCBI:284312 ∙ OMIM:620026 ∙ HGNC:23712 ∙ Uniprot:Q8NBB4 ∙ 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 ZSCAN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN1 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					1	1
missense			34	2		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	34	2	1

Variants in ZSCAN1

This is a list of pathogenic ClinVar variants found in the ZSCAN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-58037846-C-T		not specified	Uncertain significance (Dec 02, 2021)
19-58037873-C-T		not specified	Uncertain significance (Jun 17, 2022)
19-58037906-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-58037915-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-58037960-C-T		not specified	Uncertain significance (Jan 24, 2024)
19-58037986-C-A		not specified	Uncertain significance (Dec 27, 2023)
19-58038004-G-A			Benign (Dec 31, 2019)
19-58038027-G-A		not specified	Uncertain significance (May 10, 2024)
19-58038027-G-T		not specified	Uncertain significance (Sep 12, 2023)
19-58038030-A-T		not specified	Uncertain significance (Aug 17, 2022)
19-58038048-C-T		not specified	Uncertain significance (Oct 14, 2023)
19-58038127-G-T		not specified	Uncertain significance (Jan 08, 2024)
19-58038146-C-G		not specified	Uncertain significance (Nov 08, 2021)
19-58038151-C-G		not specified	Uncertain significance (Feb 27, 2024)
19-58038193-G-A		not specified	Uncertain significance (Jan 26, 2023)
19-58040468-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-58040483-A-G		not specified	Uncertain significance (Jan 24, 2023)
19-58040494-G-A		not specified	Uncertain significance (May 29, 2024)
19-58040494-G-C		not specified	Uncertain significance (Jul 14, 2022)
19-58040536-C-T		not specified	Uncertain significance (Dec 27, 2022)
19-58052514-G-A		not specified	Uncertain significance (Mar 28, 2024)
19-58052593-C-T		not specified	Uncertain significance (Nov 15, 2023)
19-58052613-G-A		not specified	Uncertain significance (Oct 04, 2022)
19-58053434-C-T		not specified	Uncertain significance (Jul 26, 2023)
19-58053435-G-A		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN1	protein_coding	protein_coding	ENST00000282326	4	20600

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.38e-7	0.224	125647	0	94	125741	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.00992	258	258	0.998	0.0000171	2620
Missense in Polyphen		61	59.89	1.0185		676
Synonymous	-0.0930	115	114	1.01	0.00000796	848
Loss of Function	0.141	10	10.5	0.953	5.02e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000722	0.000707
Ashkenazi Jewish	0.00	0.00
East Asian	0.000493	0.000489
Finnish	0.0000721	0.0000462
European (Non-Finnish)	0.000530	0.000501
Middle Eastern	0.000493	0.000489
South Asian	0.000131	0.000131
Other	0.000514	0.000489

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.847
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.69

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.146
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.413

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;protein binding;metal ion binding