GOLGA6A

golgin A6 family member A, the group of Golgin related

Basic information

Region (hg38): 15:74069857-74082550

Previous symbols: [ "GOLGA6" ]

Links

ENSG00000159289 ∙ NCBI:342096 ∙ OMIM:610288 ∙ HGNC:13567 ∙ Uniprot:Q9NYA3 ∙ 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 GOLGA6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA6A 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				2		2
missense			41	4		45
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	6	0

Variants in GOLGA6A

This is a list of pathogenic ClinVar variants found in the GOLGA6A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-74070942-C-T		not specified	Likely benign (Jul 30, 2024)
15-74070951-G-C		not specified	Uncertain significance (Dec 21, 2022)
15-74070978-C-G		not specified	Uncertain significance (Jan 16, 2024)
15-74071008-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
15-74071009-G-T		not specified	Uncertain significance (Nov 25, 2024)
15-74071037-A-G		not specified	Uncertain significance (Sep 26, 2024)
15-74071037-A-T		not specified	Likely benign (Aug 16, 2021)
15-74071128-C-A		not specified	Uncertain significance (Mar 14, 2023)
15-74071136-C-T		not specified	Uncertain significance (May 17, 2023)
15-74071146-A-C			Likely benign (Nov 01, 2023)
15-74071151-C-T		not specified	Uncertain significance (Sep 21, 2023)
15-74071159-G-T		not specified	Uncertain significance (Dec 10, 2024)
15-74071166-C-G		not specified	Likely benign (Apr 07, 2023)
15-74071198-G-A		not specified	Uncertain significance (Aug 08, 2022)
15-74071202-C-T		not specified	Uncertain significance (Oct 05, 2023)
15-74071204-A-G		not specified	Uncertain significance (Apr 09, 2024)
15-74071219-T-C		not specified	Uncertain significance (Dec 15, 2024)
15-74071227-A-C		not specified	Uncertain significance (Jun 04, 2024)
15-74071244-G-A		not specified	Uncertain significance (Feb 03, 2022)
15-74071262-G-C		not specified	Uncertain significance (Jan 03, 2024)
15-74071272-C-A		not specified	Uncertain significance (Nov 21, 2022)
15-74071369-T-C		not specified	Uncertain significance (Jul 25, 2023)
15-74071401-A-T		not specified	Uncertain significance (Dec 17, 2024)
15-74071438-C-A		not specified	Uncertain significance (Aug 05, 2023)
15-74071561-G-A			Likely benign (Dec 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA6A	protein_coding	protein_coding	ENST00000290438	18	12694

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000161	0.442	125547	0	131	125678	0.000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.294	108	99.7	1.08	0.00000588	4276
Missense in Polyphen		19	17.353	1.0949		1144
Synonymous	0.899	31	38.1	0.815	0.00000227	1163
Loss of Function	0.451	8	9.50	0.842	4.05e-7	484

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00257	0.00237
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000321	0.000317
Middle Eastern	0.00	0.00
South Asian	0.00168	0.00167
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0773

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: Golgi organization;spindle assembly
• Cellular component: Golgi cis cisterna;Golgi apparatus;cis-Golgi network;Golgi cisterna membrane