ZSCAN5A

zinc finger and SCAN domain containing 5A, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 19:56219670-56368383

Previous symbols: [ "ZNF495", "ZSCAN5" ]

Links

ENSG00000131848 ∙ NCBI:79149 ∙ ∙ HGNC:23710 ∙ Uniprot:Q9BUG6 ∙ 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 ZSCAN5A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN5A 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			34	5		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	34	5	1

Variants in ZSCAN5A

This is a list of pathogenic ClinVar variants found in the ZSCAN5A region.

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

Position	Type	Phenotype	Significance	ClinVar
19-56221585-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-56221630-C-T		not specified	Likely benign (Dec 20, 2021)
19-56221717-G-C		not specified	Likely benign (Aug 23, 2021)
19-56221820-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-56221891-C-T		not specified	Uncertain significance (Aug 02, 2021)
19-56221925-C-T		not specified	Uncertain significance (Dec 14, 2022)
19-56222021-C-T		not specified	Uncertain significance (Jul 06, 2021)
19-56222032-G-A		not specified	Uncertain significance (Mar 22, 2023)
19-56222051-C-T		not specified	Uncertain significance (Aug 16, 2022)
19-56222092-G-A		not specified	Uncertain significance (Jan 26, 2022)
19-56222108-C-T		not specified	Uncertain significance (Dec 11, 2023)
19-56222134-T-C		not specified	Uncertain significance (Dec 28, 2022)
19-56222138-C-T		not specified	Uncertain significance (Jun 24, 2022)
19-56222176-G-A		not specified	Uncertain significance (Dec 03, 2021)
19-56222180-T-C		not specified	Likely benign (Dec 03, 2021)
19-56222195-C-T		not specified	Likely benign (Apr 28, 2022)
19-56222210-C-T		not specified	Uncertain significance (May 23, 2023)
19-56222243-A-G		not specified	Uncertain significance (Jul 12, 2023)
19-56222284-A-C		not specified	Uncertain significance (Apr 25, 2024)
19-56222293-G-A		not specified	Uncertain significance (Jun 13, 2024)
19-56222593-G-A		not specified	Uncertain significance (Sep 29, 2023)
19-56222680-G-A		not specified	Uncertain significance (Sep 13, 2023)
19-56222686-A-G		not specified	Likely benign (Dec 13, 2023)
19-56222689-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-56222691-C-G		not specified	Uncertain significance (Dec 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN5A	protein_coding	protein_coding	ENST00000587340	4	147072

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00819	0.937	125715	0	3	125718	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.246	291	279	1.04	0.0000154	3256
Missense in Polyphen		69	97.302	0.70913		1248
Synonymous	-1.69	140	117	1.20	0.00000728	962
Loss of Function	1.66	5	10.9	0.458	6.34e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000186	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.06

Haploinsufficiency Scores

• pHI: 0.0921
• hipred: N
• hipred_score: 0.214
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan5b

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;metal ion binding