GCC2

GRIP and coiled-coil domain containing 2, the group of Golgins

Basic information

Region (hg38): 2:108449107-108509415

Links

ENSG00000135968 ∙ NCBI:9648 ∙ OMIM:612711 ∙ HGNC:23218 ∙ Uniprot:Q8IWJ2 ∙ 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 GCC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCC2 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				7	5	12
missense			80	10	4	94
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	80	17	10

Variants in GCC2

This is a list of pathogenic ClinVar variants found in the GCC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-108449673-G-A		not specified	Uncertain significance (Nov 29, 2024)
2-108451052-C-A		GCC2-related disorder • not specified	Uncertain significance (Aug 13, 2021)
2-108451092-A-G		not specified	Uncertain significance (Feb 28, 2024)
2-108452435-C-G		GCC2-related disorder	Benign (Jun 05, 2018)
2-108468990-A-G		not specified	Uncertain significance (Jul 14, 2023)
2-108468999-A-G		not specified	Uncertain significance (Aug 12, 2021)
2-108469005-T-C		not specified	Uncertain significance (Aug 30, 2021)
2-108469069-G-T		not specified	Uncertain significance (Apr 13, 2023)
2-108469672-G-A		not specified	Uncertain significance (Jan 23, 2023)
2-108469700-A-G		GCC2-related disorder	Likely benign (Feb 22, 2022)
2-108469714-A-G		not specified	Uncertain significance (Feb 10, 2022)
2-108469721-T-C		not specified	Uncertain significance (Aug 17, 2022)
2-108469756-T-C		not specified	Uncertain significance (Oct 12, 2024)
2-108470069-T-C		not specified	Likely benign (Dec 28, 2022)
2-108470103-G-T		not specified	Uncertain significance (Jan 23, 2023)
2-108470109-A-G		GCC2-related disorder	Benign (Jun 05, 2018)
2-108470255-C-G		not specified	Uncertain significance (Jun 03, 2024)
2-108470281-A-G		GCC2-related disorder	Likely benign (Mar 01, 2022)
2-108470303-T-G		not specified	Uncertain significance (Nov 20, 2024)
2-108470305-G-T		not specified	Uncertain significance (Aug 15, 2023)
2-108470324-A-G		not specified	Uncertain significance (May 27, 2022)
2-108470358-A-G		GCC2-related disorder	Benign (May 21, 2018)
2-108470362-G-A		not specified	Uncertain significance (Aug 14, 2024)
2-108470396-C-T		not specified	Uncertain significance (Jan 22, 2024)
2-108470399-A-G		Progressive sensorineural hearing impairment	Uncertain significance (Sep 03, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCC2	protein_coding	protein_coding	ENST00000309863	23	60855

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000199	1.00	125699	0	48	125747	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.160	791	778	1.02	0.0000386	11149
Missense in Polyphen		196	225.78	0.86809		3485
Synonymous	-1.57	316	282	1.12	0.0000141	2864
Loss of Function	6.08	26	87.2	0.298	0.00000443	1203

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000306	0.000305
Ashkenazi Jewish	0.000894	0.000893
East Asian	0.0000565	0.0000544
Finnish	0.000142	0.000139
European (Non-Finnish)	0.000171	0.000167
Middle Eastern	0.0000565	0.0000544
South Asian	0.000200	0.000196
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Golgin which probably tethers transport vesicles to the trans-Golgi network (TGN) and regulates vesicular transport between the endosomes and the Golgi. As a RAB9A effector it is involved in recycling of the mannose 6-phosphate receptor from the late endosomes to the TGN. May also play a role in transport between the recycling endosomes and the Golgi. Required for maintenance of the Golgi structure, it is involved in the biogenesis of noncentrosomal, Golgi-associated microtubules through recruitment of CLASP1 and CLASP2. {ECO:0000269|PubMed:16885419, ECO:0000269|PubMed:17488291, ECO:0000269|PubMed:17543864}.
• Pathway: Deregulation of Rab and Rab Effector Genes in Bladder Cancer;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: 0.871
• rvis_EVS: -1.63
• rvis_percentile_EVS: 2.86

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.467
• ghis: 0.605

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.468

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gcc2

Gene ontology

• Biological process: protein targeting to lysosome;microtubule organizing center organization;protein localization to Golgi apparatus;microtubule anchoring;late endosome to Golgi transport;retrograde transport, endosome to Golgi;Golgi to plasma membrane protein transport;regulation of protein exit from endoplasmic reticulum;recycling endosome to Golgi transport;Golgi ribbon formation
• Cellular component: nucleoplasm;cytoplasm;Golgi apparatus;trans-Golgi network;cytosol;membrane
• Molecular function: protein binding;identical protein binding