ZSCAN22

zinc finger and SCAN domain containing 22, the group of Zinc fingers C2H2-type|MicroRNA protein coding host genes|SCAN domain containing

Basic information

Region (hg38): 19:58326994-58342343

Previous symbols: [ "ZNF50", "HKR2" ]

Links

ENSG00000182318 ∙ NCBI:342945 ∙ OMIM:165260 ∙ HGNC:4929 ∙ Uniprot:P10073 ∙ 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 ZSCAN22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN22 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			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	2	0

Variants in ZSCAN22

This is a list of pathogenic ClinVar variants found in the ZSCAN22 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-58334816-A-G		not specified	Uncertain significance (Sep 21, 2023)
19-58334844-A-T		not specified	Uncertain significance (Feb 12, 2024)
19-58334845-G-A		not specified	Uncertain significance (Jul 09, 2021)
19-58334912-C-T		not specified	Uncertain significance (Aug 12, 2024)
19-58334920-G-C		not specified	Uncertain significance (Sep 14, 2022)
19-58334924-A-G		not specified	Uncertain significance (Feb 19, 2025)
19-58334940-G-C		not specified	Uncertain significance (Nov 21, 2022)
19-58334954-G-C		not specified	Uncertain significance (Nov 13, 2024)
19-58334972-A-G		not specified	Uncertain significance (Jan 23, 2024)
19-58335004-G-A		not specified	Uncertain significance (Feb 06, 2023)
19-58335014-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-58335017-C-T		not specified	Uncertain significance (May 09, 2024)
19-58335086-A-T		not specified	Uncertain significance (Dec 25, 2024)
19-58338337-A-G		not specified	Uncertain significance (Nov 14, 2023)
19-58338340-C-T		not specified	Uncertain significance (Jul 30, 2023)
19-58338345-G-A		not specified	Uncertain significance (Nov 26, 2024)
19-58338424-G-A		not specified	Uncertain significance (Feb 12, 2025)
19-58338476-G-A		not specified	Uncertain significance (Sep 16, 2021)
19-58338487-G-A		not specified	Uncertain significance (Jun 07, 2023)
19-58338511-C-T		not specified	Likely benign (Jan 08, 2024)
19-58338512-G-A		not specified	Uncertain significance (Dec 17, 2023)
19-58338512-G-C		not specified	Uncertain significance (Oct 30, 2023)
19-58338527-C-T		not specified	Likely benign (Mar 01, 2025)
19-58338533-A-G		not specified	Uncertain significance (Jan 09, 2024)
19-58338539-C-G		not specified	Uncertain significance (Feb 19, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN22	protein_coding	protein_coding	ENST00000329665	2	15314

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.25e-8	0.501	125671	0	77	125748	0.000306

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.219	282	293	0.964	0.0000180	3196
Missense in Polyphen		67	70.49	0.95049		800
Synonymous	0.166	124	126	0.981	0.00000846	984
Loss of Function	0.921	13	17.1	0.760	0.00000109	185

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000513	0.000510
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000380	0.000378
Middle Eastern	0.000109	0.000109
South Asian	0.000196	0.000196
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.122

Intolerance Scores

• loftool: 0.771
• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.82

Haploinsufficiency Scores

• pHI: 0.176
• hipred: N
• hipred_score: 0.146
• ghis: 0.538

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.950

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan22

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;biological_process
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;molecular_function;DNA binding;protein binding;metal ion binding