GOLGA5

golgin A5, the group of Golgins

Basic information

Region (hg38): 14:92794304-92839947

Links

ENSG00000066455 ∙ NCBI:9950 ∙ OMIM:606918 ∙ HGNC:4428 ∙ Uniprot:Q8TBA6 ∙ 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 GOLGA5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA5 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						0
missense			33	3		36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	34	3	0

Variants in GOLGA5

This is a list of pathogenic ClinVar variants found in the GOLGA5 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-92797540-A-G		not specified	Uncertain significance (Apr 19, 2023)
14-92797556-C-T		not specified	Uncertain significance (Jan 31, 2023)
14-92797597-T-G		not specified	Uncertain significance (May 03, 2023)
14-92797602-G-C		not specified	Uncertain significance (Aug 16, 2021)
14-92797751-G-C		not specified	Uncertain significance (Aug 15, 2023)
14-92797767-T-G		not specified	Uncertain significance (May 28, 2024)
14-92797768-G-T		not specified	Uncertain significance (Jul 11, 2023)
14-92797943-A-G		not specified	Uncertain significance (Nov 21, 2023)
14-92797957-A-C		not specified	Uncertain significance (Mar 25, 2024)
14-92797958-A-G		not specified	Uncertain significance (Nov 12, 2021)
14-92806794-T-A		not specified	Uncertain significance (Nov 09, 2021)
14-92806823-A-C		not specified	Uncertain significance (Dec 07, 2021)
14-92806846-G-A		not specified	Likely benign (Mar 01, 2023)
14-92806915-A-C		not specified	Uncertain significance (Mar 21, 2023)
14-92806958-A-G		not specified	Uncertain significance (May 24, 2024)
14-92806964-G-T			Uncertain significance (Oct 03, 2023)
14-92809479-C-T		not specified	Uncertain significance (Nov 27, 2023)
14-92809480-G-A		not specified	Uncertain significance (Apr 05, 2023)
14-92810262-A-G		not specified	Uncertain significance (Apr 10, 2023)
14-92810307-C-G		not specified	Uncertain significance (Mar 01, 2023)
14-92810361-G-A		not specified	Uncertain significance (Mar 28, 2024)
14-92811554-G-A			Likely benign (Jul 11, 2018)
14-92811563-G-A		not specified	Uncertain significance (Aug 10, 2021)
14-92811567-G-A		not specified	Uncertain significance (Aug 23, 2021)
14-92811591-G-A		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA5	protein_coding	protein_coding	ENST00000163416	12	45733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000596	1.00	125727	0	21	125748	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.718	343	383	0.897	0.0000197	4804
Missense in Polyphen		70	93.123	0.75169		1197
Synonymous	0.504	132	140	0.946	0.00000721	1369
Loss of Function	4.11	16	46.1	0.347	0.00000312	452

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000908	0.0000904
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.000219	0.000217
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000107	0.000105
Middle Eastern	0.000219	0.000217
South Asian	0.00	0.00
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in maintaining Golgi structure. Stimulates the formation of Golgi stacks and ribbons. Involved in intra-Golgi retrograde transport. {ECO:0000269|PubMed:12538640, ECO:0000269|PubMed:15718469}.
• Disease: DISEASE: Note=A chromosomal aberration involving GOLGA5 is found in papillary thyroid carcinomas (PTCs). Translocation t(10;14)(q11;q32) with RET. The translocation generates the RET/GOLGA5 (PTC5) oncogene. {ECO:0000269|PubMed:2734021, ECO:0000269|PubMed:9443391}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;TCR;Intra-Golgi traffic;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.140

Intolerance Scores

• loftool: 0.516
• rvis_EVS: 0.27
• rvis_percentile_EVS: 70.69

Haploinsufficiency Scores

• pHI: 0.194
• hipred: Y
• hipred_score: 0.557
• ghis: 0.499

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golga5
• Phenotype: craniofacial phenotype; growth/size/body region phenotype; skeleton phenotype; digestive/alimentary phenotype

Gene ontology

• Biological process: retrograde transport, vesicle recycling within Golgi;Golgi organization;Golgi vesicle transport
• Cellular component: Golgi membrane;Golgi apparatus;cis-Golgi network;membrane;integral component of membrane;transport vesicle;Golgi cisterna
• Molecular function: Rab GTPase binding;protein homodimerization activity