ZSCAN2

zinc finger and SCAN domain containing 2, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 15:84600986-84627796

Previous symbols: [ "ZFP29" ]

Links

ENSG00000176371 ∙ NCBI:54993 ∙ ∙ HGNC:20994 ∙ Uniprot:Q7Z7L9 ∙ 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 ZSCAN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN2 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			51	4		55
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	51	5	0

Variants in ZSCAN2

This is a list of pathogenic ClinVar variants found in the ZSCAN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-84603944-T-G		not specified	Uncertain significance (Jan 23, 2023)
15-84603947-C-T		not specified	Uncertain significance (Feb 14, 2023)
15-84603952-G-A		not specified	Uncertain significance (Jan 06, 2023)
15-84603975-G-C		not specified	Uncertain significance (Aug 15, 2023)
15-84604033-G-A		not specified	Uncertain significance (Sep 12, 2023)
15-84604037-A-G		not specified	Uncertain significance (Nov 12, 2021)
15-84604064-T-C		not specified	Uncertain significance (Dec 12, 2023)
15-84604078-CCT-C		Abnormality of neuronal migration	Benign (Oct 31, 2014)
15-84604084-T-A		not specified	Uncertain significance (Dec 26, 2023)
15-84604117-G-A		not specified	Likely benign (Jul 26, 2022)
15-84604145-C-G		not specified	Uncertain significance (Aug 31, 2023)
15-84604150-G-A		not specified	Uncertain significance (Jun 16, 2024)
15-84604154-C-A		not specified	Uncertain significance (Feb 13, 2024)
15-84604163-G-A		not specified	Uncertain significance (Dec 20, 2023)
15-84604169-G-A		not specified	Uncertain significance (May 13, 2024)
15-84604230-G-T		not specified	Uncertain significance (Jun 26, 2023)
15-84604231-C-G		not specified	Uncertain significance (Jun 26, 2023)
15-84604248-G-C		not specified	Uncertain significance (Apr 08, 2024)
15-84604263-G-T		not specified	Uncertain significance (Sep 12, 2023)
15-84604268-G-A		not specified	Uncertain significance (Aug 12, 2021)
15-84604310-T-C		not specified	Uncertain significance (Oct 27, 2023)
15-84604315-C-G		not specified	Uncertain significance (Sep 01, 2021)
15-84620665-G-A		not specified	Likely benign (Apr 13, 2023)
15-84620675-C-A		not specified	Uncertain significance (Dec 13, 2022)
15-84620677-C-G		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN2	protein_coding	protein_coding	ENST00000448803	2	26811

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000356	0.989	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.102	361	356	1.02	0.0000206	4132
Missense in Polyphen		187	212.73	0.87904		2520
Synonymous	-1.84	165	138	1.20	0.00000853	1112
Loss of Function	2.28	11	22.7	0.485	0.00000124	264

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000387	0.000387
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000109	0.000109
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation during the post-meiotic stages of spermatogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.583
• rvis_EVS: -1.19
• rvis_percentile_EVS: 5.86

Haploinsufficiency Scores

• pHI: 0.696
• hipred: N
• hipred_score: 0.199
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.242

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan2
• Phenotype: hematopoietic system phenotype

Gene ontology

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