ZSCAN5B

zinc finger and SCAN domain containing 5B, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56189686-56197815

Links

ENSG00000197213 ∙ NCBI:342933 ∙ ∙ HGNC:34246 ∙ Uniprot:A6NJL1 ∙ 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 ZSCAN5B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN5B 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				2		2
missense			64	8		72
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	10	0

Variants in ZSCAN5B

This is a list of pathogenic ClinVar variants found in the ZSCAN5B region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56189864-C-T		not specified	Uncertain significance (Jan 19, 2025)
19-56189865-G-A		not specified	Uncertain significance (Jan 23, 2024)
19-56189886-G-A		not specified	Uncertain significance (Mar 14, 2023)
19-56189923-C-G		not specified	Uncertain significance (Jun 16, 2024)
19-56189928-C-T		not specified	Uncertain significance (Jan 19, 2025)
19-56189930-G-A		not specified	Uncertain significance (Jul 13, 2021)
19-56189932-G-T		not specified	Uncertain significance (Apr 25, 2022)
19-56189962-C-A		not specified	Uncertain significance (Jul 26, 2024)
19-56190002-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-56190005-C-T		not specified	Likely benign (Feb 28, 2024)
19-56190008-T-C		not specified	Uncertain significance (May 28, 2024)
19-56190012-C-G		not specified	Uncertain significance (Aug 02, 2021)
19-56190015-T-C		not specified	Uncertain significance (Jan 29, 2025)
19-56190029-T-A		not specified	Uncertain significance (Nov 08, 2024)
19-56190038-A-G		not specified	Uncertain significance (Oct 03, 2024)
19-56190054-C-T		not specified	Likely benign (Apr 25, 2023)
19-56190062-T-G		not specified	Uncertain significance (Mar 21, 2023)
19-56190079-C-A		not specified	Uncertain significance (Dec 17, 2021)
19-56190098-G-A		not specified	Uncertain significance (Mar 06, 2025)
19-56190101-T-C		not specified	Uncertain significance (Nov 16, 2022)
19-56190110-T-G		not specified	Uncertain significance (Dec 15, 2023)
19-56190117-C-G		not specified	Uncertain significance (Nov 15, 2024)
19-56190144-G-A		not specified	Uncertain significance (Jan 30, 2024)
19-56190151-A-C		not specified	Uncertain significance (Feb 12, 2025)
19-56190152-C-A		not specified	Uncertain significance (Feb 12, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN5B	protein_coding	protein_coding	ENST00000586855	4	8351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00e-12	0.00601	125674	0	74	125748	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.50	403	284	1.42	0.0000163	3226
Missense in Polyphen		140	100.62	1.3914		1267
Synonymous	-0.790	126	115	1.09	0.00000707	964
Loss of Function	-1.10	16	11.9	1.34	6.93e-7	117

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00164	0.00163
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000163	0.000158
Middle Eastern	0.0000547	0.0000544
South Asian	0.000211	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in transcriptional regulation. {ECO:0000250}.

Intolerance Scores

• loftool: 0.965
• rvis_EVS: 1.76
• rvis_percentile_EVS: 96.73

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0455

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan5b

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