ZGPAT

zinc finger CCCH-type and G-patch domain containing, the group of Zinc fingers CCCH-type|G-patch domain containing

Basic information

Region (hg38): 20:63707465-63736142

Previous symbols: [ "KIAA1847" ]

Links

ENSG00000197114 ∙ NCBI:84619 ∙ OMIM:619577 ∙ HGNC:15948 ∙ Uniprot:Q8N5A5 ∙ 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 ZGPAT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ZGPAT 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			35	3		38
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	36	3	0

Variants in ZGPAT

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

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

Position	Type	Phenotype	Significance	ClinVar
20-63708590-G-A		not specified	Uncertain significance (Sep 01, 2021)
20-63708594-G-C		not specified	Uncertain significance (Nov 27, 2023)
20-63708641-G-A		not specified	Uncertain significance (Dec 21, 2022)
20-63708765-T-C		not specified	Uncertain significance (May 10, 2022)
20-63708803-G-A		not specified	Uncertain significance (Feb 17, 2022)
20-63708869-C-G		not specified	Uncertain significance (Feb 14, 2023)
20-63708894-C-T		not specified	Uncertain significance (Jan 23, 2024)
20-63708974-A-T		not specified	Uncertain significance (Dec 08, 2023)
20-63709014-T-A		not specified	Uncertain significance (Oct 13, 2023)
20-63709067-G-T		not specified	Uncertain significance (Feb 06, 2023)
20-63709088-C-G		not specified	Uncertain significance (Sep 14, 2022)
20-63709145-C-T		not specified	Uncertain significance (Jun 06, 2023)
20-63733271-C-T		not specified	Uncertain significance (Oct 03, 2022)
20-63733295-G-A		not specified	Uncertain significance (Jul 06, 2021)
20-63733337-G-A		not specified	Uncertain significance (Dec 22, 2023)
20-63733621-C-A		not specified	Uncertain significance (Dec 14, 2023)
20-63733676-C-T		not specified	Uncertain significance (Mar 02, 2023)
20-63733697-G-A		not specified	Uncertain significance (Jun 16, 2023)
20-63733731-A-G		not specified	Uncertain significance (Sep 16, 2021)
20-63734659-G-A		not specified	Uncertain significance (Mar 27, 2023)
20-63734735-C-A		not specified	Uncertain significance (Apr 08, 2023)
20-63734743-T-C		not specified	Uncertain significance (Jul 14, 2023)
20-63734744-C-G		not specified	Uncertain significance (May 07, 2024)
20-63735222-A-G		not specified	Uncertain significance (May 08, 2024)
20-63735291-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ZGPAT	protein_coding	protein_coding	ENST00000328969	6	28678

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000383	0.991	125709	0	38	125747	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.208	310	320	0.967	0.0000199	3364
Missense in Polyphen		87	107.48	0.80948		1222
Synonymous	-0.275	149	145	1.03	0.00000982	1124
Loss of Function	2.31	9	20.2	0.445	0.00000107	226

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000146	0.000139
European (Non-Finnish)	0.000211	0.000202
Middle Eastern	0.000109	0.000109
South Asian	0.000140	0.000131
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription repressor that specifically binds the 5'- GGAG[GA]A[GA]A-3' consensus sequence. Represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. Negatively regulates expression of EGFR, a gene involved in cell proliferation, survival and migration. Its ability to repress genes of the EGFR pathway suggest it may act as a tumor suppressor. Able to suppress breast carcinogenesis. {ECO:0000269|PubMed:19644445}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• rvis_EVS: -0.71
• rvis_percentile_EVS: 14.67

Haploinsufficiency Scores

• pHI: 0.149
• hipred: N
• hipred_score: 0.146
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Zgpat
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;negative regulation of epidermal growth factor-activated receptor activity;negative regulation of transcription, DNA-templated
• Cellular component: nucleus;plasma membrane
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;sequence-specific DNA binding;metal ion binding