ZSCAN10

zinc finger and SCAN domain containing 10, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 16:3088890-3099295

Previous symbols: [ "ZNF206" ]

Links

ENSG00000130182 ∙ NCBI:84891 ∙ OMIM:618365 ∙ HGNC:12997 ∙ Uniprot:Q96SZ4 ∙ 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 ZSCAN10 gene.

• ZSCAN10 Deficiency;Global developmental delay;Sensorineural hearing loss disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN10 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				3	3	6
missense			50	7	1	58
nonsense	1					1
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	2	0	50	10	4

Highest pathogenic variant AF is 0.00000657

Variants in ZSCAN10

This is a list of pathogenic ClinVar variants found in the ZSCAN10 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3089108-G-T		not specified	Uncertain significance (Mar 07, 2024)
16-3089189-C-A			Likely benign (Feb 01, 2023)
16-3089192-C-G		not specified	Uncertain significance (Oct 20, 2021)
16-3089239-C-G		not specified	Uncertain significance (Feb 07, 2023)
16-3089266-G-A		not specified	Uncertain significance (Oct 16, 2023)
16-3089270-G-T		not specified	Uncertain significance (Aug 28, 2023)
16-3089283-C-T			Likely benign (Mar 01, 2022)
16-3089288-C-G		not specified	Uncertain significance (Feb 16, 2023)
16-3089314-C-T		not specified	Uncertain significance (Jan 04, 2024)
16-3089328-G-T		not specified	Uncertain significance (Jun 11, 2021)
16-3089346-A-G			Likely benign (Mar 28, 2018)
16-3089383-TG-T		Sensorineural hearing loss disorder;ZSCAN10 Deficiency;Global developmental delay • Otofacial neurodevelopmental syndrome	Pathogenic (Apr 05, 2022)
16-3089389-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-3089511-C-G		not specified	Uncertain significance (Mar 01, 2023)
16-3089551-T-C		not specified	Uncertain significance (Jan 26, 2022)
16-3089617-T-G		not specified	Uncertain significance (Jun 07, 2023)
16-3089624-G-A		not specified	Uncertain significance (Dec 16, 2023)
16-3089764-C-T		not specified	Uncertain significance (Dec 16, 2022)
16-3089792-G-A		not specified	Uncertain significance (Jun 10, 2024)
16-3089803-T-G		not specified	Uncertain significance (May 08, 2023)
16-3089839-C-T		not specified	Uncertain significance (Sep 29, 2023)
16-3089867-C-T		not specified	Uncertain significance (Jun 17, 2022)
16-3089878-C-T		not specified	Uncertain significance (May 17, 2023)
16-3089903-C-T		not specified	Uncertain significance (Apr 28, 2023)
16-3089933-C-A		not specified	Uncertain significance (Jan 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN10	protein_coding	protein_coding	ENST00000252463	5	10428

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000804	0.997	125689	0	58	125747	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.506	456	487	0.935	0.0000370	4613
Missense in Polyphen		186	214.2	0.86836		1999
Synonymous	-1.14	247	225	1.10	0.0000177	1514
Loss of Function	2.57	11	24.9	0.443	0.00000123	248

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000987	0.0000906
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000574	0.0000544
Finnish	0.00178	0.00176
European (Non-Finnish)	0.000133	0.000123
Middle Eastern	0.0000574	0.0000544
South Asian	0.0000330	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Embryonic stem (ES) cell-specific transcription factor required to maintain ES cell pluripotency. Can both activate and /or repress expression of target genes, depending on the context. Specifically binds the 5'-[GA]CGCNNGCG[CT]-3' DNA consensus sequence. Regulates expression of POU5F1/OCT4, ZSCAN4 and ALYREF/THOC4. {ECO:0000250|UniProtKB:Q3URR7}.
• Pathway: Developmental Biology;Transcriptional regulation of pluripotent stem cells (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.490
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.36

Haploinsufficiency Scores

• pHI: 0.480
• hipred: N
• hipred_score: 0.326
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.320

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan10
• Phenotype: renal/urinary system phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;somatic stem cell population maintenance;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;sequence-specific DNA binding;metal ion binding