GOLGA6D
protein-codinggolgin A6 family member D, the group of Golgin related
Gene summary
Predicted to be involved in Golgi organization. Predicted to be located in Golgi apparatus. Predicted to be active in Golgi cis cisterna; Golgi cisterna membrane; and cis-Golgi network. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~12.7 kbGenCC 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 GOLGA6D variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001145224.3. 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 | 1 | ||||
| missense | 75 | 14 | 89 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 75 | 15 | 0 | 90 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001138696.1 | 18 | MANE Select | |
| Ensembl | ENSP00000391085.3 | 18 | MANE Select | |
| RefSeq | XP_047288921.1 | 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:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000434739
- Coding exons
- 18
- Length
- 11641
- Individuals with no LoFs
- 123678
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 85
- Defined
- 123764
- p
- 0.000347
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.796 | 102 | 81.8 | 1.25 | 0.00000480 | 4448 |
| Missense (PolyPhen) | 24 | 21.701 | 1.1059 | 1086 | ||
| Synonymous | -2.52 | 54 | 35.0 | 1.54 | 0.00000218 | 1248 |
| Loss of Function | -1.18 | 9 | 5.90 | 1.53 | 2.87e-7 | 494 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00018 | 0.00015 | rare |
| Ashkenazi Jewish | 0.0040 | 0.0039 | notable |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00033 | 0.00031 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0.00069 | 0.00066 | rare |
dbNSFP Gene Annotations
Source:
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0886
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |