GCC1

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

Basic information

Region (hg38): 7:127580628-127593611

Links

ENSG00000179562 ∙ NCBI:79571 ∙ OMIM:607418 ∙ HGNC:19095 ∙ Uniprot:Q96CN9 ∙ 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 GCC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCC1 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				1		1
missense			58	2		60
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	58	3	0

Variants in GCC1

This is a list of pathogenic ClinVar variants found in the GCC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-127582046-T-G		not specified	Uncertain significance (Jan 31, 2024)
7-127582049-T-C		not specified	Likely benign (Sep 07, 2024)
7-127582055-G-A		not specified	Uncertain significance (Jun 13, 2024)
7-127582068-T-G		not specified	Uncertain significance (Apr 07, 2022)
7-127582081-G-A		not specified	Uncertain significance (Feb 27, 2024)
7-127582111-G-C		not specified	Uncertain significance (Jan 22, 2025)
7-127582228-T-A		not specified	Uncertain significance (Feb 13, 2023)
7-127582255-C-T		not specified	Uncertain significance (Jan 23, 2025)
7-127582282-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-127582308-C-A		not specified	Uncertain significance (Dec 04, 2024)
7-127582312-A-C		not specified	Uncertain significance (Nov 03, 2022)
7-127582358-G-A		not specified	Uncertain significance (Dec 28, 2024)
7-127582394-C-T		not specified	Uncertain significance (Jan 24, 2024)
7-127582396-T-C		not specified	Likely benign (Apr 07, 2022)
7-127582399-G-T		not specified	Uncertain significance (Feb 22, 2023)
7-127582423-G-A		not specified	Uncertain significance (Aug 13, 2021)
7-127582435-G-C		not specified	Uncertain significance (Aug 27, 2024)
7-127582446-G-T		not specified	Uncertain significance (Dec 06, 2024)
7-127582535-G-C		not specified	Uncertain significance (Feb 05, 2025)
7-127582571-G-A		not specified	Uncertain significance (Aug 30, 2021)
7-127582637-G-A		not specified	Uncertain significance (Jan 23, 2025)
7-127582652-G-A		not specified	Uncertain significance (Sep 26, 2024)
7-127582684-T-C		not specified	Uncertain significance (Jan 10, 2025)
7-127582806-G-C		not specified	Uncertain significance (May 27, 2022)
7-127582820-T-C		not specified	Uncertain significance (Jan 28, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCC1	protein_coding	protein_coding	ENST00000321407	2	12994

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000145	0.991	125692	0	56	125748	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.633	399	436	0.915	0.0000257	5053
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000283	0.000281
Middle Eastern	0.000435	0.000435
South Asian	0.000229	0.000229
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably involved in maintaining Golgi structure.
• Pathway: Nuclear Receptors Meta-Pathway;Vesicle-mediated transport;Membrane Trafficking;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.759
• rvis_EVS: 0.25
• rvis_percentile_EVS: 69.57

Haploinsufficiency Scores

• pHI: 0.203
• hipred: N
• hipred_score: 0.335
• ghis: 0.550

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.883

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcc1

Gene ontology

• Cellular component: Golgi membrane;Golgi apparatus;cytosol;plasma membrane
• Molecular function: protein binding