ZSCAN21

zinc finger and SCAN domain containing 21, the group of Zinc fingers C2H2-type|SCAN domain containing

Basic information

Region (hg38): 7:100049774-100065040

Previous symbols: [ "ZNF38" ]

Links

ENSG00000166529 ∙ NCBI:7589 ∙ OMIM:601261 ∙ HGNC:13104 ∙ Uniprot:Q9Y5A6 ∙ 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 ZSCAN21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN21 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			27	3		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	3	0

Variants in ZSCAN21

This is a list of pathogenic ClinVar variants found in the ZSCAN21 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-100057085-A-G		not specified	Uncertain significance (May 11, 2022)
7-100057113-A-G		not specified	Uncertain significance (Apr 15, 2022)
7-100057133-A-G		not specified	Uncertain significance (Jun 10, 2024)
7-100057139-C-T		not specified	Uncertain significance (Dec 21, 2022)
7-100057140-G-T		not specified	Uncertain significance (Jan 10, 2023)
7-100057143-A-G		not specified	Uncertain significance (Jan 03, 2022)
7-100057185-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-100057320-T-C		not specified	Uncertain significance (May 05, 2023)
7-100057367-G-A		not specified	Uncertain significance (Dec 01, 2022)
7-100057379-C-T		not specified	Uncertain significance (Apr 01, 2024)
7-100057380-G-A		not specified	Likely benign (May 05, 2023)
7-100057397-G-C		not specified	Uncertain significance (May 24, 2024)
7-100057398-G-C		not specified	Uncertain significance (Jun 03, 2024)
7-100057738-A-C		not specified	Uncertain significance (Sep 06, 2022)
7-100057800-A-G		not specified	Uncertain significance (Aug 02, 2022)
7-100057849-G-T		not specified	Uncertain significance (Jul 29, 2022)
7-100057865-C-A		not specified	Uncertain significance (Feb 27, 2023)
7-100063811-G-A		not specified	Uncertain significance (Oct 12, 2022)
7-100063814-G-C		not specified	Uncertain significance (Apr 17, 2024)
7-100063958-C-G		not specified	Uncertain significance (Mar 28, 2024)
7-100063977-A-C		not specified	Uncertain significance (Sep 21, 2023)
7-100063991-G-A		not specified	Likely benign (Mar 20, 2023)
7-100064021-C-T		not specified	Uncertain significance (Nov 29, 2023)
7-100064027-A-G		not specified	Uncertain significance (Jan 23, 2024)
7-100064040-G-C		not specified	Uncertain significance (Apr 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN21	protein_coding	protein_coding	ENST00000292450	3	15272

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.48e-12	0.0457	125667	0	80	125747	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.246	258	269	0.958	0.0000147	3107
Missense in Polyphen		93	97.897	0.94998		1160
Synonymous	-0.146	107	105	1.02	0.00000620	878
Loss of Function	0.133	18	18.6	0.967	9.45e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000756	0.000753
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.0000476	0.0000462
European (Non-Finnish)	0.000320	0.000316
Middle Eastern	0.000598	0.000598
South Asian	0.000439	0.000425
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Strong transcriptional activator. {ECO:0000250}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.707
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.88

Haploinsufficiency Scores

• pHI: 0.108
• hipred: N
• hipred_score: 0.195
• ghis: 0.544

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.460

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan21
• Phenotype: normal phenotype; reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;metal ion binding