GPATCH2

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

Basic information

Region (hg38): 1:217426991-217631090

Previous symbols: [ "GPATC2" ]

Links

ENSG00000092978 ∙ NCBI:55105 ∙ OMIM:616836 ∙ HGNC:25499 ∙ Uniprot:Q9NW75 ∙ 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 GPATCH2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPATCH2 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		1
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	2	0

Variants in GPATCH2

This is a list of pathogenic ClinVar variants found in the GPATCH2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-217431205-TC-T		Long QT syndrome	Likely benign (-)
1-217431302-T-C		not specified	Likely benign (May 09, 2023)
1-217431323-A-G		not specified	Uncertain significance (Dec 07, 2021)
1-217431329-T-C		not specified	Uncertain significance (Mar 20, 2024)
1-217491717-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-217498375-G-A		not specified	Uncertain significance (Apr 08, 2024)
1-217610332-G-T		not specified	Uncertain significance (Dec 03, 2021)
1-217610338-C-T		not specified	Uncertain significance (Sep 06, 2022)
1-217610353-T-C		not specified	Uncertain significance (Jan 23, 2023)
1-217610949-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-217610976-T-C		not specified	Uncertain significance (Jul 05, 2023)
1-217610994-A-T		not specified	Uncertain significance (Mar 29, 2023)
1-217619798-T-C		not specified	Uncertain significance (Jan 07, 2022)
1-217619828-A-G		not specified	Uncertain significance (Apr 25, 2022)
1-217619837-T-G		not specified	Uncertain significance (Nov 10, 2022)
1-217619949-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-217619957-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-217619968-A-C		not specified	Uncertain significance (Apr 05, 2023)
1-217620033-T-A		not specified	Uncertain significance (Feb 01, 2023)
1-217620081-G-A		not specified	Uncertain significance (May 06, 2024)
1-217620142-C-T			Likely benign (Nov 01, 2022)
1-217620152-T-C		not specified	Uncertain significance (Jul 20, 2021)
1-217620163-G-C		not specified	Uncertain significance (Jan 24, 2023)
1-217620173-G-A		not specified	Uncertain significance (Jun 06, 2022)
1-217620309-C-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPATCH2	protein_coding	protein_coding	ENST00000366935	10	204091

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-11	0.480	125691	0	57	125748	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.03	241	291	0.829	0.0000150	3482
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000592	0.000592
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000225	0.000220
Middle Eastern	0.000109	0.000109
South Asian	0.000272	0.000261
Other	0.000328	0.000326

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.358
• hipred: N
• hipred_score: 0.454
• ghis: 0.549

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.507

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpatch2

Gene ontology

• Biological process: negative regulation of phosphatase activity
• Cellular component: nucleolus;nuclear speck
• Molecular function: nucleic acid binding