GPATCH2

protein-coding

G-patch domain containing 2, the group of G-patch domain containing|Protein phosphatase 1 regulatory subunits|SSU processome

Gene summary

The gene encodes a nuclear factor that may play a role in spermatogenesis and in tumor growth during breast cancer. The encoded protein contains a G-patch domain with an RNA binding motif. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]

Previous symbols:

GPATC2

MANE transcript

NM_018040.5

Inheritance

—

ClinVar variants

U:67B:5

Top phenotype

Long QT syndrome

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr1:217,426,992-217,631,090

External References & Databases

Ensembl (ENSG00000092978)

Transcript & Mutation Effects

hg38 • Region Span ~204.1 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 GPATCH2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 64

not providedTotal: 1

Long QT syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018040.5. 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			4 clinvar	1 clinvar		5
missense			62 clinvar	3 clinvar		65
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	67	5	0	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018040.5	RefSeq	NP_060510.1	10	MANE Select
ENST00000366935.8	Ensembl	ENSP00000355902.3	10	MANE Select
NM_001297754.3	RefSeq	NP_001284683.1	6	Standard
ENST00000366934.3	Ensembl	ENSP00000355901.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of phosphatase activity

Molecular Function

nucleic acid binding

Cellular Component

nucleolus
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000366935
Coding exons: 10
Length: 204091
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 57
Defined: 125748
p: 0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.03	241	291	0.829	0.0000150	3482
Missense (PolyPhen)		95	105.88	0.89721		1246
Synonymous	0.704	91	99.9	0.910	0.00000525	978
Loss of Function	1.29	21	28.4	0.739	0.00000165	316

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00041	0.00040	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00022	0.00022	rare
South Asian	0.00027	0.00026	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Enhances the ATPase activity of DHX15 in vitro. {ECO:0000269|PubMed:19432882}.;

Intolerance Scores

LoFtool: 0.905
RVIS EVS: 0.11
RVIS percentile EVS: 61.91

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.507

Gene Damage Prediction

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