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.

• not_specified (132 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000018025.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			128	4	2	134
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	128	4	2

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