GPATCH1

G-patch domain containing 1, the group of G-patch domain containing|Spliceosomal Bact complex|Spliceosomal C complex

Basic information

Region (hg38): 19:33080899-33130542

Previous symbols: [ "GPATC1" ]

Links

ENSG00000076650 ∙ NCBI:55094 ∙ ∙ HGNC:24658 ∙ Uniprot:Q9BRR8 ∙ 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 GPATCH1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPATCH1 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			54	2	2	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	2	2

Variants in GPATCH1

This is a list of pathogenic ClinVar variants found in the GPATCH1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-33081245-G-C		not specified	Uncertain significance (Nov 09, 2021)
19-33088149-A-T		not specified	Uncertain significance (Mar 16, 2024)
19-33088203-G-T		not specified	Uncertain significance (Jun 01, 2023)
19-33088211-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-33088223-G-A		not specified	Uncertain significance (Nov 18, 2022)
19-33088251-C-G		not specified	Uncertain significance (Apr 22, 2022)
19-33090801-T-C		not specified	Uncertain significance (Mar 27, 2023)
19-33090821-G-A		not specified	Uncertain significance (Apr 12, 2022)
19-33090831-C-A		not specified	Uncertain significance (Oct 29, 2021)
19-33093435-T-C		not specified	Uncertain significance (May 29, 2024)
19-33093438-G-A		not specified	Uncertain significance (Sep 06, 2022)
19-33093461-G-A		not specified	Uncertain significance (Feb 28, 2023)
19-33093465-C-A		not specified	Uncertain significance (Feb 15, 2023)
19-33093473-C-T		not specified	Uncertain significance (Jan 31, 2024)
19-33093479-C-T		not specified	Uncertain significance (Feb 27, 2023)
19-33094188-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-33094219-G-T		not specified	Uncertain significance (Dec 27, 2022)
19-33094224-G-A		not specified	Uncertain significance (Mar 15, 2024)
19-33094227-G-A		not specified	Likely benign (Apr 19, 2024)
19-33094248-C-T		not specified	Uncertain significance (Mar 15, 2024)
19-33094254-C-T		not specified	Uncertain significance (Jan 04, 2022)
19-33096262-C-T		not specified	Uncertain significance (Apr 09, 2024)
19-33096338-T-G		not specified	Uncertain significance (Apr 23, 2024)
19-33096369-A-G		not specified	Likely benign (Jun 30, 2022)
19-33096376-G-A		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPATCH1	protein_coding	protein_coding	ENST00000170564	20	49663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.55e-11	1.00	125664	0	84	125748	0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.679	484	528	0.917	0.0000296	6058
Missense in Polyphen		102	114.68	0.88946		1302
Synonymous	0.997	189	207	0.912	0.0000128	1794
Loss of Function	3.41	27	54.0	0.500	0.00000321	624

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000790	0.000789
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000551	0.000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000336	0.000334
Middle Eastern	0.000551	0.000544
South Asian	0.000461	0.000457
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.888
• rvis_EVS: -0.21
• rvis_percentile_EVS: 37.76

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.426
• ghis: 0.546

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.526

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpatch1

Gene ontology

• Biological process: mRNA splicing, via spliceosome
• Cellular component: nucleus;catalytic step 2 spliceosome
• Molecular function: RNA binding