GOLGA6B

protein-coding

golgin A6 family member B, the group of Golgin related

Gene summary

This gene is found in a large, low copy repeat sequence or duplicon that is found in multiple copies, which are greater than 90% similar, on chromosome 15. Duplicons are associated with deletions, inversions and other chromosomal rearrangements that underlie genomic disease. This gene is a member of the golgin gene family, whose protein products localize to the Golgi apparatus. The majority of the related gene copies are thought to be transcribed pseudogenes. It is not known whether this gene is a pseudogene or if it encodes a golgin protein. [provided by RefSeq, Jul 2008]

MANE transcript

NM_018652.5

Inheritance

—

ClinVar variants

U:102B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.15

Max pathogenic AF

—

Genomic locus

chr15:72,654,697-72,669,599

External References & Databases

Ensembl (ENSG00000215186)

Transcript & Mutation Effects

hg38 • Region Span ~14.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GOLGA6B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018652.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar		4
missense			100 clinvar	5 clinvar		105
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	8	0	110

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018652.5	RefSeq	NP_061122.4	18	MANE Select
ENST00000421285.4	Ensembl	ENSP00000408132.3	18	MANE Select
ENST00000909077.1	Ensembl	ENSP00000579136.1	18	Standard
ENST00000909077.2	Ensembl	ENSP00000579136.1	18	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

Golgi organization
spindle assembly

Cellular Component

Golgi cis cisterna
Golgi apparatus
cis-Golgi network
Golgi cisterna membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000421285
Coding exons: 18
Length: 11657
Individuals with no LoFs: 125523
Homozygous LoFs: 7
Heterozygous LoFs: 119
Defined: 125649
p: 0.000502

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.600	181	160	1.13	0.00000889	4357
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0028	0.0020	notable
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00019	0.00016	rare
Finnish	0.000053	0.000046	rare
European (Non-Finnish)	0.00075	0.00070	rare
South Asian	0	0.0	absent
Other	0.00068	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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