GOLGA6B

golgin A6 family member B, the group of Golgin related

Basic information

Region (hg38): 15:72654697-72669599

Links

ENSG00000215186 ∙ NCBI:55889 ∙ ∙ HGNC:32205 ∙ Uniprot:A6NDN3 ∙ 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 GOLGA6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA6B 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				3		3
missense			46	4		50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	46	7	0

Variants in GOLGA6B

This is a list of pathogenic ClinVar variants found in the GOLGA6B region.

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

Position	Type	Phenotype	Significance	ClinVar
15-72661298-G-A		not specified	Uncertain significance (Apr 06, 2024)
15-72661322-G-A			Likely benign (Feb 01, 2024)
15-72661335-C-T			Likely benign (Nov 01, 2024)
15-72661459-G-A		not specified	Uncertain significance (Dec 16, 2024)
15-72661493-G-A		not specified	Uncertain significance (Dec 21, 2022)
15-72661531-C-G		not specified	Uncertain significance (Nov 21, 2024)
15-72661531-C-T		not specified	Uncertain significance (Feb 13, 2023)
15-72662270-C-T		not specified	Uncertain significance (Jan 14, 2025)
15-72662276-C-T		not specified	Uncertain significance (May 14, 2024)
15-72662315-C-T		not specified	Uncertain significance (Mar 07, 2023)
15-72662335-G-T		not specified	Uncertain significance (Aug 08, 2022)
15-72662342-G-T		not specified	Uncertain significance (Nov 08, 2022)
15-72662363-C-G		not specified	Uncertain significance (Jan 09, 2025)
15-72662383-G-A		not specified	Uncertain significance (Feb 13, 2025)
15-72662383-G-C		not specified	Uncertain significance (Jan 11, 2023)
15-72662404-G-A		not specified	Uncertain significance (Oct 12, 2021)
15-72662420-T-C		not specified	Uncertain significance (Feb 07, 2025)
15-72662426-A-G		not specified	Uncertain significance (Nov 12, 2024)
15-72662444-G-A		not specified	Uncertain significance (Feb 12, 2025)
15-72662452-G-C		not specified	Uncertain significance (Dec 28, 2022)
15-72662467-C-T		not specified	Uncertain significance (Apr 06, 2022)
15-72662496-C-T			Likely benign (Jul 01, 2022)
15-72662506-C-T		not specified	Uncertain significance (Dec 13, 2022)
15-72662522-C-T		not specified	Uncertain significance (Jun 02, 2023)
15-72662530-G-A		not specified	Uncertain significance (Dec 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA6B	protein_coding	protein_coding	ENST00000421285	18	11657

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.26e-12	0.0132	125523	7	119	125649	0.000502

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.600	181	160	1.13	0.00000889	4357
Missense in Polyphen		32	33.998	0.94122		677
Synonymous	-0.739	75	67.3	1.11	0.00000393	1204
Loss of Function	-0.527	17	14.8	1.15	7.36e-7	483

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00296	0.00216
Ashkenazi Jewish	0.00	0.00
East Asian	0.000192	0.000163
Finnish	0.0000534	0.0000462
European (Non-Finnish)	0.000746	0.000704
Middle Eastern	0.000192	0.000163
South Asian	0.00	0.00
Other	0.000684	0.000652

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0696
• hipred: N
• hipred_score: 0.431

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