ZSCAN16

zinc finger and SCAN domain containing 16, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 6:28107689-28130082

Previous symbols: [ "ZNF392", "ZNF435" ]

Links

ENSG00000196812 ∙ NCBI:80345 ∙ OMIM:618544 ∙ HGNC:20813 ∙ Uniprot:Q9H4T2 ∙ 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 ZSCAN16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN16 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			18	1		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	0

Variants in ZSCAN16

This is a list of pathogenic ClinVar variants found in the ZSCAN16 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-28125540-A-C		not specified	Uncertain significance (Sep 14, 2023)
6-28125628-T-G		not specified	Uncertain significance (Nov 09, 2021)
6-28125689-C-A		not specified	Uncertain significance (Feb 28, 2023)
6-28125705-C-A		not specified	Uncertain significance (Aug 19, 2023)
6-28125747-C-T		not specified	Uncertain significance (Sep 28, 2021)
6-28125796-A-G		not specified	Uncertain significance (Sep 14, 2022)
6-28125822-G-A		not specified	Likely benign (Jun 26, 2023)
6-28126872-T-A		not specified	Uncertain significance (Oct 12, 2021)
6-28126896-G-C		not specified	Uncertain significance (Nov 17, 2023)
6-28129490-A-G		not specified	Uncertain significance (Jul 15, 2021)
6-28129542-T-G		not specified	Uncertain significance (Apr 23, 2024)
6-28129628-G-C		not specified	Uncertain significance (Apr 19, 2023)
6-28129699-T-C		not specified	Uncertain significance (Feb 27, 2023)
6-28129702-G-A		not specified	Uncertain significance (Dec 26, 2023)
6-28129780-A-C		not specified	Uncertain significance (Jun 11, 2021)
6-28129817-C-G		not specified	Uncertain significance (Sep 27, 2022)
6-28129838-G-A		not specified	Uncertain significance (Jan 16, 2024)
6-28129861-T-C		not specified	Uncertain significance (May 08, 2023)
6-28129880-G-A		not specified	Uncertain significance (Jan 26, 2022)
6-28129910-T-C		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN16	protein_coding	protein_coding	ENST00000340487	3	5523

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.13e-7	0.275	125420	5	321	125746	0.00130

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.788	154	184	0.837	0.00000924	2295
Missense in Polyphen		45	59.302	0.75882		745
Synonymous	1.21	54	66.6	0.811	0.00000321	636
Loss of Function	0.377	11	12.4	0.885	5.23e-7	175

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00115
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000178	0.000167
Middle Eastern	0.000381	0.000381
South Asian	0.00899	0.00886
Other	0.000817	0.000815

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.728
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.215
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

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