GOLGA4

golgin A4, the group of Golgins

Basic information

Region (hg38): 3:37243190-37366879

Links

ENSG00000144674 ∙ NCBI:2803 ∙ OMIM:602509 ∙ HGNC:4427 ∙ Uniprot:Q13439 ∙ 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 GOLGA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA4 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			110	12	5	127
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	110	12	6

Variants in GOLGA4

This is a list of pathogenic ClinVar variants found in the GOLGA4 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-37251396-C-A		not specified	Uncertain significance (Jun 29, 2023)
3-37251396-C-T		not specified	Uncertain significance (Jun 18, 2021)
3-37251413-A-G		not specified	Uncertain significance (Oct 27, 2023)
3-37251459-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-37251463-T-A		not specified	Uncertain significance (Nov 07, 2022)
3-37273555-C-T		not specified	Uncertain significance (Nov 05, 2021)
3-37273591-G-A		not specified	Uncertain significance (Feb 14, 2024)
3-37281968-C-T			Benign (May 30, 2018)
3-37281997-C-T		not specified	Uncertain significance (Sep 27, 2021)
3-37281998-G-A		not specified	Uncertain significance (Dec 17, 2021)
3-37282079-G-A		not specified	Uncertain significance (Sep 26, 2023)
3-37282133-G-A		not specified	Likely benign (Sep 16, 2021)
3-37282162-G-A		not specified	Uncertain significance (Apr 09, 2024)
3-37282165-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-37282219-C-T		not specified	Likely benign (Jun 16, 2024)
3-37282229-G-A		not specified	Uncertain significance (Apr 26, 2024)
3-37282234-G-A		not specified	Uncertain significance (Oct 30, 2023)
3-37282252-T-A		not specified	Uncertain significance (Sep 26, 2023)
3-37296147-C-T		not specified	Uncertain significance (May 30, 2023)
3-37296189-G-A		not specified	Uncertain significance (May 13, 2024)
3-37296190-A-T		not specified	Uncertain significance (Apr 22, 2022)
3-37296210-G-A		not specified	Uncertain significance (Apr 15, 2024)
3-37296216-G-T		GOLGA4-related disorder	Likely benign (Feb 16, 2022)
3-37298844-A-G		not specified	Likely benign (Mar 05, 2024)
3-37298886-C-T		not specified	Uncertain significance (Jan 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA4	protein_coding	protein_coding	ENST00000356847	23	123575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.48e-16	1.00	125531	1	216	125748	0.000863

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.103	1081	1.07e+3	1.01	0.0000534	14924
Missense in Polyphen		319	344.42	0.9262		5150
Synonymous	-0.594	400	385	1.04	0.0000188	3793
Loss of Function	5.95	47	116	0.404	0.00000613	1530

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00114	0.00112
Ashkenazi Jewish	0.000321	0.000298
East Asian	0.000606	0.000598
Finnish	0.000324	0.000323
European (Non-Finnish)	0.000513	0.000501
Middle Eastern	0.000606	0.000598
South Asian	0.00420	0.00350
Other	0.00124	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in vesicular trafficking at the Golgi apparatus level. May play a role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with MACF1. Involved in endosome-to-Golgi trafficking (PubMed:29084197). {ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:29084197}.
• 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: 0.191

Intolerance Scores

• loftool: 0.918
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.05

Haploinsufficiency Scores

• pHI: 0.310
• hipred: N
• hipred_score: 0.361
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.649

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golga4

Gene ontology

• Biological process: vesicle-mediated transport;Golgi to plasma membrane protein transport;positive regulation of axon extension
• Cellular component: Golgi membrane;cytoplasm;Golgi apparatus;trans-Golgi network;cytosol;intracellular membrane-bounded organelle;extracellular exosome
• Molecular function: protein binding;GTPase binding