ZSCAN9

zinc finger and SCAN domain containing 9, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 6:28224886-28233487

Previous symbols: [ "ZNF193" ]

Links

ENSG00000137185 ∙ NCBI:7746 ∙ OMIM:602246 ∙ HGNC:12984 ∙ Uniprot:O15535 ∙ 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 ZSCAN9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN9 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						0
missense			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in ZSCAN9

This is a list of pathogenic ClinVar variants found in the ZSCAN9 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28227136-G-T		not specified	Uncertain significance (Aug 19, 2023)
6-28227239-G-A		not specified	Uncertain significance (Mar 28, 2024)
6-28227249-T-A		not specified	Uncertain significance (Apr 27, 2024)
6-28227286-G-A		not specified	Uncertain significance (Nov 09, 2023)
6-28227407-T-C		not specified	Uncertain significance (Mar 06, 2023)
6-28227426-A-C		not specified	Uncertain significance (Nov 03, 2023)
6-28227449-A-G		not specified	Uncertain significance (Apr 13, 2023)
6-28227724-G-A		not specified	Uncertain significance (Aug 17, 2022)
6-28227760-T-G		not specified	Uncertain significance (Jul 27, 2023)
6-28227772-C-T		not specified	Uncertain significance (Jan 05, 2022)
6-28230405-C-G		not specified	Uncertain significance (Dec 12, 2023)
6-28230441-T-C		not specified	Uncertain significance (Dec 14, 2023)
6-28232631-A-G		not specified	Uncertain significance (Feb 03, 2022)
6-28232654-A-G		not specified	Uncertain significance (Apr 25, 2023)
6-28232693-G-A		not specified	Uncertain significance (Aug 02, 2023)
6-28232705-A-C		not specified	Uncertain significance (Apr 17, 2024)
6-28232796-G-T		not specified	Uncertain significance (Oct 29, 2021)
6-28232802-T-C		not specified	Uncertain significance (Dec 16, 2022)
6-28232816-A-G		not specified	Uncertain significance (Feb 05, 2024)
6-28232862-C-G		not specified	Uncertain significance (May 29, 2024)
6-28232895-G-A		not specified	Likely benign (Jun 27, 2022)
6-28232936-T-C		not specified	Uncertain significance (Sep 22, 2022)
6-28233041-C-T		not specified	Uncertain significance (Jul 26, 2022)
6-28233042-G-A		not specified	Uncertain significance (Dec 30, 2023)
6-28233084-G-A		not specified	Uncertain significance (Apr 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN9	protein_coding	protein_coding	ENST00000425468	4	8597

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.72e-11	0.114	125710	0	37	125747	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.624	211	238	0.886	0.0000118	2931
Missense in Polyphen		78	76.344	1.0217		951
Synonymous	0.697	76	84.1	0.903	0.00000388	839
Loss of Function	0.504	18	20.5	0.880	0.00000132	205

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000365	0.000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.000272	0.000272
South Asian	0.000294	0.000294
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0773

Intolerance Scores

• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.0614
• hipred: N
• hipred_score: 0.112
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

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