GPATCH2

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

Basic information

Region (hg38): 1:217426992-217631090

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.

• not_specified (55 variants)
• not_provided (1 variants)
• Long_QT_syndrome (1 variants)

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. These statistics are base on transcript: NM_000018040.5. 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				1		1
missense			53	2		55
nonsense						0
start loss						0
frameshift				1		1
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	4	0

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