GeneBe

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

  • otofacial neurodevelopmental syndrome (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Otofacial neurodevelopmental syndromeARAudiologic/Otolaryngologic; CardiovascularAmong other findings, the condition can involve hearing loss, and early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; The condition can include congenital anomalies, including cardiovascular anomalies, and awareness may allow early difentificaitons and managementAudiologic/Otolaryngologic; Cardiovascular; Craniofacial; Genitourinary; Neurologic38386308

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ZSCAN10 gene.

  • not_specified (119 variants)
  • not_provided (9 variants)
  • Otofacial_neurodevelopmental_syndrome (5 variants)
  • ZSCAN10_Deficiency (2 variants)
  • Global_developmental_delay (2 variants)
  • 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. These statistics are base on transcript: NM_000032805.3. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
3
clinvar
 7
missense
112
clinvar
9
clinvar
 121
nonsense
2
clinvar
 2
start loss
0
frameshift
3
clinvar
 3
splice donor/acceptor (+/-2bp)
0
Total 5 0 112 13 3

Highest pathogenic variant AF is 0.000029055578

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ZSCAN10protein_codingprotein_codingENST00000252463 510428
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.00008040.9971256890581257470.000231
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.5064564870.9350.00003704613
Missense in Polyphen186214.20.868361999
Synonymous-1.142472251.100.00001771514
Loss of Function2.571124.90.4430.00000123248

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00009870.0000906
Ashkenazi Jewish0.0001010.0000992
East Asian0.00005740.0000544
Finnish0.001780.00176
European (Non-Finnish)0.0001330.000123
Middle Eastern0.00005740.0000544
South Asian0.00003300.0000327
Other0.0001630.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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