GOPC

protein-coding

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

Gene summary

This gene encodes a Golgi protein with a PDZ domain. The PDZ domain is globular and proteins which contain them bind other proteins through short motifs near the C-termini. Mice which are deficient in the orthologous protein have globozoospermia and are infertile. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]

MANE transcript

NM_020399.4

Inheritance

—

ClinVar variants

U:63B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr6:117,560,269-117,602,542

External References & Databases

Ensembl (ENSG00000047932)

Transcript & Mutation Effects

hg38 • Region Span ~42.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GOPC variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 62

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020399.4. 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			2 clinvar	2 clinvar		4
missense			61 clinvar	2 clinvar		63
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	63	4	0	67

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020399.4	RefSeq	NP_065132.1	9	MANE Select
ENST00000368498.7	Ensembl	ENSP00000357484.2	9	MANE Select
NM_001017408.3	RefSeq	NP_001017408.1	8	Standard
ENST00000052569.10	Ensembl	ENSP00000052569.6	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signal Transduction
RHO GTPases regulate CFTR trafficking
RHO GTPase Effectors
Signaling by Rho GTPases

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

Molecular Function

protein binding
ion channel binding

Cellular Component

Golgi membrane
cytoplasm
lysosomal membrane
Golgi apparatus
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368498
Coding exons: 9
Length: 284318
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125747
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.88	163	246	0.663	0.0000123	3003
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00018	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.131

Intolerance Scores

LoFtool: 0.622
RVIS EVS: -0.63
RVIS percentile EVS: 17.03

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.752

Gene Damage Prediction

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