GPATCH3

G-patch domain containing 3, the group of G-patch domain containing

Basic information

Region (hg38): 1:26890487-26900467

Previous symbols: [ "GPATC3" ]

Links

ENSG00000198746 ∙ NCBI:63906 ∙ OMIM:617486 ∙ HGNC:25720 ∙ Uniprot:Q96I76 ∙ 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 GPATCH3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPATCH3 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				3		3
missense			35	2		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	35	5	0

Variants in GPATCH3

This is a list of pathogenic ClinVar variants found in the GPATCH3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-26891119-G-A		not specified	Uncertain significance (Jun 05, 2023)
1-26891164-C-T			Uncertain significance (May 25, 2017)
1-26891202-T-C		GPATCH3-related disorder	Likely benign (May 03, 2019)
1-26891208-T-C		GPATCH3-related disorder	Likely benign (Mar 28, 2019)
1-26892705-C-T		not specified	Uncertain significance (Oct 04, 2022)
1-26892752-C-T		not specified	Uncertain significance (Dec 28, 2022)
1-26892755-A-G		not specified	Uncertain significance (Jul 12, 2023)
1-26892777-C-T		not specified	Uncertain significance (Aug 02, 2021)
1-26892786-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-26893439-T-C		not specified	Uncertain significance (Jan 25, 2023)
1-26894262-G-A		not specified	Uncertain significance (May 29, 2024)
1-26894343-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-26894353-C-T		not specified	Likely benign (Apr 12, 2023)
1-26894359-C-T		not specified	Uncertain significance (Dec 20, 2022)
1-26894390-T-A		not specified	Uncertain significance (Nov 07, 2022)
1-26894400-C-A		not specified	Uncertain significance (May 03, 2023)
1-26894401-G-C		not specified	Uncertain significance (Dec 28, 2023)
1-26897317-T-A		not specified	Uncertain significance (Jun 18, 2021)
1-26897395-T-A		not specified	Uncertain significance (Jan 23, 2023)
1-26897402-T-C		not specified	Uncertain significance (Mar 01, 2023)
1-26897417-C-T		not specified	Uncertain significance (Mar 11, 2022)
1-26897476-T-C		GPATCH3-related disorder	Likely benign (Jul 16, 2019)
1-26897480-C-G		not specified	Uncertain significance (Aug 15, 2023)
1-26897537-G-A		not specified	Uncertain significance (Nov 20, 2023)
1-26897539-G-C		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPATCH3	protein_coding	protein_coding	ENST00000361720	7	9979

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.40e-14	0.0595	125532	0	216	125748	0.000859

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.226	327	316	1.04	0.0000183	3379
Missense in Polyphen		119	115.44	1.0308		1191
Synonymous	-0.213	127	124	1.02	0.00000626	1099
Loss of Function	0.534	22	24.9	0.885	0.00000125	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000593	0.000593
Ashkenazi Jewish	0.000599	0.000595
East Asian	0.000109	0.000109
Finnish	0.000925	0.000832
European (Non-Finnish)	0.00127	0.00126
Middle Eastern	0.000109	0.000109
South Asian	0.000817	0.000817
Other	0.000981	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in transcriptional regulation. It is able to activate transcription from the CXCR4 promoter and therefore it might control neural crest cell migration involved in ocular and craniofacial development (PubMed:28397860). Is a negative regulator of immune antiviral response, acting via down-regulation of RIG-I-like receptors signaling and inhibition of type I interferon production. The control mechanism involves interaction with mitochondrial MAVS and inhibition of MAVS assembly with downstream proteins implicated in antiviral response, such as TBK1 and TRAF6 (PubMed:28414768). {ECO:0000269|PubMed:28397860, ECO:0000269|PubMed:28414768}.

Intolerance Scores

• loftool: 0.924
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.8

Haploinsufficiency Scores

• pHI: 0.0540
• hipred: N
• hipred_score: 0.167
• ghis: 0.523

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.931

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpatch3

Zebrafish Information Network

• Gene name: gpatch3
• Affected structure: iridophore
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of type I interferon production;negative regulation of RIG-I signaling pathway;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;cytoplasm
• Molecular function: nucleic acid binding;protein binding