ZSCAN29

zinc finger and SCAN domain containing 29, the group of SCAN domain containing|Zinc fingers C2H2-type

Basic information

Region (hg38): 15:43358171-43371043

Previous symbols: [ "ZNF690" ]

Links

ENSG00000140265 ∙ NCBI:146050 ∙ ∙ HGNC:26673 ∙ Uniprot:Q8IWY8 ∙ 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 ZSCAN29 gene.

• Inborn genetic diseases (30 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZSCAN29 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					1	1
missense			28	1		29
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4	3	7
Total	0	0	29	5	4

Variants in ZSCAN29

This is a list of pathogenic ClinVar variants found in the ZSCAN29 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-43361123-C-T		ZSCAN29-related disorder • not specified	Benign/Likely benign (Feb 23, 2023)
15-43361124-G-A			Benign (Nov 06, 2020)
15-43361171-G-A		not specified	Uncertain significance (Dec 20, 2023)
15-43361179-T-C		not specified	Uncertain significance (Aug 08, 2023)
15-43361194-G-A		not specified	Uncertain significance (Jan 22, 2024)
15-43361205-A-G		ZSCAN29-related disorder	Likely benign (Sep 25, 2019)
15-43361240-T-A		not specified	Uncertain significance (Dec 18, 2023)
15-43361251-T-G		not specified	Uncertain significance (Sep 22, 2022)
15-43361336-C-G		not specified	Uncertain significance (Dec 14, 2023)
15-43361348-A-G		not specified	Uncertain significance (Nov 17, 2022)
15-43361417-A-G		not specified	Uncertain significance (Feb 03, 2022)
15-43361434-G-C		not specified	Uncertain significance (Oct 20, 2023)
15-43361451-G-A		ZSCAN29-related disorder	Benign (Oct 21, 2019)
15-43361485-C-T		not specified	Uncertain significance (Dec 19, 2022)
15-43361542-C-T		not specified	Uncertain significance (May 09, 2023)
15-43361566-C-T		not specified	Uncertain significance (Feb 16, 2023)
15-43361567-G-A		not specified	Uncertain significance (Jul 26, 2021)
15-43361621-A-C		not specified	Uncertain significance (Sep 23, 2023)
15-43361653-A-C		ZSCAN29-related disorder	Likely benign (Jul 01, 2019)
15-43361681-A-G		not specified	Uncertain significance (Oct 04, 2022)
15-43361682-G-A		ZSCAN29-related disorder	Likely benign (Jul 23, 2019)
15-43361688-C-G		not specified	Uncertain significance (Dec 12, 2023)
15-43361740-G-A		not specified	Uncertain significance (Nov 21, 2022)
15-43361746-G-C		not specified	Uncertain significance (Apr 13, 2022)
15-43361800-C-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZSCAN29	protein_coding	protein_coding	ENST00000396976	5	12854

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.03e-10	0.911	125642	0	106	125748	0.000422

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0638	470	474	0.992	0.0000264	5611
Missense in Polyphen		175	187.26	0.93454		2259
Synonymous	0.243	165	169	0.976	0.00000849	1617
Loss of Function	1.93	21	32.9	0.638	0.00000169	425

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00141	0.00141
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000475	0.000466
Middle Eastern	0.000326	0.000326
South Asian	0.000528	0.000523
Other	0.00	0.00

dbNSFP

Source: dbNSFP

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

Intolerance Scores

• loftool: 0.904
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.25

Haploinsufficiency Scores

• pHI: 0.217
• hipred: N
• hipred_score: 0.154
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0251

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zscan29

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