GOPC

golgi associated PDZ and coiled-coil motif containing, the group of PDZ domain containing

Basic information

Region (hg38): 6:117560269-117602542

Links

ENSG00000047932 ∙ NCBI:57120 ∙ OMIM:606845 ∙ HGNC:17643 ∙ Uniprot:Q9HD26 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GOPC gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOPC 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				2		2
missense			30	2		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	4	0

Variants in GOPC

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

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

Position	Type	Phenotype	Significance	ClinVar
6-117563258-T-C		not specified	Uncertain significance (Feb 08, 2025)
6-117563273-T-C		not specified	Uncertain significance (Dec 28, 2022)
6-117563285-A-G		not specified	Uncertain significance (Jun 11, 2021)
6-117563306-C-T		not specified	Uncertain significance (Oct 12, 2024)
6-117563307-C-T		not specified	Likely benign (Apr 04, 2024)
6-117563328-T-G		not specified	Uncertain significance (Feb 13, 2024)
6-117563378-T-C		not specified	Uncertain significance (Jan 18, 2022)
6-117566875-C-G		not specified	Uncertain significance (Dec 13, 2023)
6-117566893-T-G		not specified	Uncertain significance (Oct 07, 2024)
6-117566905-T-A		not specified	Uncertain significance (Mar 07, 2025)
6-117566937-C-T		not specified	Uncertain significance (Apr 20, 2024)
6-117566938-G-A		not specified	Uncertain significance (Mar 28, 2024)
6-117566946-T-C		not specified	Uncertain significance (Jan 19, 2025)
6-117566953-T-G		not specified	Uncertain significance (Dec 27, 2023)
6-117566978-A-G			Likely benign (May 01, 2022)
6-117569601-T-C		not specified	Uncertain significance (Mar 19, 2024)
6-117569694-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-117569712-T-C		not specified	Uncertain significance (Sep 01, 2021)
6-117570865-T-C		not specified	Uncertain significance (Feb 05, 2024)
6-117573522-C-T		not specified	Uncertain significance (Aug 22, 2023)
6-117573529-C-T		not specified	Uncertain significance (Sep 02, 2024)
6-117573606-C-T		not specified	Uncertain significance (May 10, 2024)
6-117575258-C-T		not specified	Uncertain significance (Nov 24, 2024)
6-117575299-T-G		not specified	Uncertain significance (Dec 31, 2024)
6-117575345-T-C		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOPC	protein_coding	protein_coding	ENST00000368498	9	284318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000843	0.996	125717	0	30	125747	0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.88	163	246	0.663	0.0000123	3003
Missense in Polyphen		26	79.464	0.32719		964
Synonymous	0.990	81	93.2	0.869	0.00000478	906
Loss of Function	2.61	9	22.3	0.403	0.00000123	267

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000247	0.000243
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000181	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000177	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in intracellular protein trafficking and degradation. May regulate CFTR chloride currents and acid-induced ASIC3 currents by modulating cell surface expression of both channels. May also regulate the intracellular trafficking of the ADR1B receptor. May play a role in autophagy. Overexpression results in CFTR intracellular retention and degradation in the lysosomes. {ECO:0000269|PubMed:11707463, ECO:0000269|PubMed:14570915, ECO:0000269|PubMed:15358775}.
• Disease: DISEASE: Note=A chromosomal aberration involving GOPC is found in a glioblastoma multiforme sample. An intra-chromosomal deletion del(6)(q21q21) is responsible for the formation of GOPC-ROS1 chimeric protein which has a constitutive receptor tyrosine kinase activity. {ECO:0000269|PubMed:12661006}.
• Pathway: Signal Transduction;RHO GTPases regulate CFTR trafficking;RHO GTPase Effectors;Signaling by Rho GTPases (Consensus)

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.622
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.581
• hipred: Y
• hipred_score: 0.693
• ghis: 0.700

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.752

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gopc
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;Golgi to plasma membrane transport;negative regulation of anion channel activity;protein transport;cytoplasmic sequestering of CFTR protein;apical protein localization;protein homooligomerization;negative regulation of protein localization to cell surface
• Cellular component: Golgi membrane;cytoplasm;lysosomal membrane;Golgi apparatus;plasma membrane;postsynaptic density;membrane;cell junction;trans-Golgi network transport vesicle;dendrite;Golgi-associated vesicle membrane;protein-containing complex;postsynaptic membrane
• Molecular function: protein binding;ion channel binding