GPATCH2L

G-patch domain containing 2 like

Basic information

Region (hg38): 14:76151916-76254342

Previous symbols: [ "C14orf118" ]

Links

ENSG00000089916 ∙ NCBI:55668 ∙ ∙ HGNC:20210 ∙ Uniprot:Q9NWQ4 ∙ 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 GPATCH2L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPATCH2L 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						0
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	17	1	0

Variants in GPATCH2L

This is a list of pathogenic ClinVar variants found in the GPATCH2L region.

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

Position	Type	Phenotype	Significance	ClinVar
14-76154376-G-A		not specified	Uncertain significance (Dec 17, 2023)
14-76154488-G-T		not specified	Uncertain significance (Nov 10, 2024)
14-76154545-A-T		not specified	Uncertain significance (Dec 15, 2023)
14-76154624-C-G		not specified	Uncertain significance (Nov 09, 2021)
14-76154737-C-T		not specified	Uncertain significance (Jul 07, 2024)
14-76154785-C-T		not specified	Uncertain significance (Aug 12, 2022)
14-76154915-G-T		not specified	Uncertain significance (May 18, 2023)
14-76166710-A-G		not specified	Uncertain significance (Jan 26, 2023)
14-76172005-G-A		not specified	Uncertain significance (Jan 26, 2023)
14-76173552-A-G		not specified	Uncertain significance (Jun 18, 2021)
14-76173612-G-A		not specified	Uncertain significance (Mar 19, 2024)
14-76176676-C-A		not specified	Uncertain significance (Sep 20, 2023)
14-76176680-C-T		not specified	Uncertain significance (Sep 05, 2024)
14-76177923-C-T			Likely benign (Mar 01, 2023)
14-76180806-G-A		not specified	Uncertain significance (May 14, 2024)
14-76180819-G-A		not specified	Uncertain significance (May 11, 2022)
14-76195880-A-G		not specified	Uncertain significance (May 23, 2023)
14-76195894-T-C		not specified	Uncertain significance (Jun 09, 2022)
14-76195942-G-A		not specified	Uncertain significance (Nov 15, 2021)
14-76201720-C-T		not specified	Uncertain significance (Jul 31, 2023)
14-76201736-C-G		not specified	Uncertain significance (Jul 12, 2023)
14-76201739-A-G		not specified	Uncertain significance (Jul 06, 2021)
14-76201846-A-G		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPATCH2L	protein_coding	protein_coding	ENST00000261530	9	102427

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00282	0.997	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.04	227	276	0.824	0.0000157	3143
Missense in Polyphen		95	127.77	0.7435		1413
Synonymous	-0.885	108	96.9	1.11	0.00000503	946
Loss of Function	3.38	10	30.0	0.334	0.00000209	284

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000367	0.000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000709	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.000366	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.177
• hipred: N
• hipred_score: 0.492
• ghis: 0.574

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpatch2l

Gene ontology

• Molecular function: protein binding