GCC1

protein-coding

GRIP and coiled-coil domain containing 1, the group of Golgins

Gene summary

The protein encoded by this gene is a peripheral membrane protein. It is sensitive to brefeldin A. This encoded protein contains a GRIP domain which is thought to be used in targeting. It may play a role in the organization of trans-Golgi network subcompartment involved with membrane transport. [provided by RefSeq, Jul 2008]

MANE transcript

NM_024523.6

Inheritance

—

ClinVar variants

U:109B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr7:127,580,628-127,593,611

External References & Databases

Ensembl (ENSG00000179562)

Transcript & Mutation Effects

hg38 • Region Span ~13.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GCC1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 111

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024523.6. 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				1 clinvar		1
missense			109 clinvar	2 clinvar		111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	109	3	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024523.6	RefSeq	NP_078799.2	2	MANE Select
ENST00000321407.3	Ensembl	ENSP00000318821.2	2	MANE Select
ENST00001127735.1	Ensembl	ENSP00000797540.1	2	Standard
ENST00001140324.1	Ensembl	ENSP00000806614.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Nuclear Receptors Meta-Pathway
Vesicle-mediated transport
Membrane Trafficking
Retrograde transport at the Trans-Golgi-Network
Intra-Golgi and retrograde Golgi-to-ER traffic

Molecular Function

protein binding

Cellular Component

Golgi membrane
Golgi apparatus
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321407
Coding exons: 2
Length: 12994
Individuals with no LoFs: 125692
Homozygous LoFs: 0
Heterozygous LoFs: 56
Defined: 125748
p: 0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.633	399	436	0.915	0.0000257	5053
Missense (PolyPhen)		115	131.79	0.87258		1571
Synonymous	-0.133	180	178	1.01	0.00000936	1569
Loss of Function	2.37	14	27.4	0.512	0.00000144	320

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00043	0.00044	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00028	0.00028	rare
South Asian	0.00023	0.00023	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probably involved in maintaining Golgi structure.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.759
RVIS EVS: 0.25
RVIS percentile EVS: 69.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.883

Gene Damage Prediction

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