GPATCH1

protein-coding

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

Gene summary

Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Part of catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

GPATC1

MANE transcript

NM_018025.3

Inheritance

—

ClinVar variants

U:150B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.5

Max pathogenic AF

—

Genomic locus

chr19:33,080,899-33,130,542

External References & Databases

Ensembl (ENSG00000076650)

Transcript & Mutation Effects

hg38 • Region Span ~49.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GPATCH1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 142

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018025.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			144 clinvar	4 clinvar	2 clinvar	150
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	150	4	2	156

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018025.3	RefSeq	NP_060495.2	20	MANE Select
ENST00000170564.7	Ensembl	ENSP00000170564.1	20	MANE Select
ENST00000592165.1	Ensembl	ENSP00000467632.1	5	Standard
ENST00000880979.1	Ensembl	ENSP00000551038.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

mRNA splicing, via spliceosome

Molecular Function

RNA binding

Cellular Component

nucleus
catalytic step 2 spliceosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000170564
Coding exons: 20
Length: 49663
Individuals with no LoFs: 125664
Homozygous LoFs: 0
Heterozygous LoFs: 84
Defined: 125748
p: 0.000334

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.679	484	528	0.917	0.0000296	6058
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00048	0.00046	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00055	0.00054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00034	0.00033	rare
South Asian	0.00046	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.888
RVIS EVS: -0.21
RVIS percentile EVS: 37.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.526

Gene Damage Prediction

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