GPATCH4

G-patch domain containing 4 (gene/pseudogene), the group of G-patch domain containing

Basic information

Region (hg38): 1:156594301-156601496

Previous symbols: [ "GPATC4" ]

Links

ENSG00000160818 ∙ NCBI:54865 ∙ ∙ HGNC:25982 ∙ Uniprot:Q5T3I0 ∙ 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 GPATCH4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPATCH4 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	2		3
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	32	2	0

Variants in GPATCH4

This is a list of pathogenic ClinVar variants found in the GPATCH4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-156595292-T-C		not specified	Uncertain significance (Jul 05, 2022)
1-156595319-C-A		not specified	Uncertain significance (Mar 03, 2022)
1-156595332-G-C		not specified	Uncertain significance (Oct 22, 2021)
1-156595379-G-A		not specified	Uncertain significance (Feb 15, 2023)
1-156595416-C-T		not specified	Uncertain significance (Aug 19, 2024)
1-156595464-T-C		not specified	Uncertain significance (Sep 11, 2024)
1-156595489-G-C		not specified	Uncertain significance (Aug 20, 2024)
1-156595593-T-A		not specified	Uncertain significance (Jun 07, 2023)
1-156595594-T-C			Likely benign (Mar 01, 2025)
1-156595661-C-T		not specified	Uncertain significance (Mar 18, 2024)
1-156595670-G-A		not specified	Uncertain significance (Aug 02, 2023)
1-156595703-T-G		not specified	Uncertain significance (Apr 06, 2024)
1-156595729-G-T		not specified	Uncertain significance (Aug 11, 2022)
1-156595730-C-A		not specified	Uncertain significance (Oct 04, 2022)
1-156595732-C-G		not specified	Uncertain significance (Dec 16, 2023)
1-156595754-C-T		not specified	Uncertain significance (Aug 05, 2024)
1-156595776-G-A		not specified	Uncertain significance (Apr 27, 2023)
1-156595809-G-A		not specified	Uncertain significance (Oct 25, 2024)
1-156595826-A-T		not specified	Uncertain significance (Jan 05, 2022)
1-156596443-G-T		not specified	Uncertain significance (Feb 08, 2025)
1-156596456-C-G		not specified	Uncertain significance (Apr 25, 2022)
1-156597920-C-T			Uncertain significance (Jul 01, 2022)
1-156598071-A-G			Likely benign (Dec 01, 2024)
1-156598087-G-T		not specified	Uncertain significance (Mar 18, 2024)
1-156598102-C-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPATCH4	protein_coding	protein_coding	ENST00000438976	8	7010

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000569	0.710	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.704	169	197	0.859	0.0000102	2496
Missense in Polyphen		41	45.958	0.89212		595
Synonymous	1.68	51	68.7	0.742	0.00000341	656
Loss of Function	0.981	8	11.6	0.689	4.91e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000558	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000361	0.0000352
Middle Eastern	0.0000558	0.0000544
South Asian	0.000346	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0790

Intolerance Scores

• loftool: 0.437
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.1

Haploinsufficiency Scores

• pHI: 0.0575
• hipred: N
• hipred_score: 0.123
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.497

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpatch4

Gene ontology

• Molecular function: RNA binding;protein binding