GOLGA6D

golgin A6 family member D, the group of Golgin related

Basic information

Region (hg38): 15:75282835-75295530

Links

ENSG00000140478 ∙ NCBI:653643 ∙ ∙ HGNC:32204 ∙ Uniprot:P0CG33 ∙ 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 GOLGA6D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLGA6D 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			37	7		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	7	0

Variants in GOLGA6D

This is a list of pathogenic ClinVar variants found in the GOLGA6D region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75288083-A-C		not specified	Uncertain significance (Aug 10, 2021)
15-75288129-A-G		not specified	Uncertain significance (Jun 27, 2022)
15-75288150-G-A		not specified	Uncertain significance (Dec 25, 2024)
15-75288282-G-A		not specified	Uncertain significance (Jul 05, 2023)
15-75288303-A-G		not specified	Likely benign (Apr 27, 2022)
15-75288321-G-A		not specified	Uncertain significance (Aug 16, 2021)
15-75288326-C-G		not specified	Uncertain significance (Oct 04, 2022)
15-75288330-G-C		not specified	Likely benign (Mar 07, 2023)
15-75288342-C-T		not specified	Uncertain significance (Sep 16, 2021)
15-75288363-G-A		not specified	Likely benign (Nov 13, 2024)
15-75289427-C-T		not specified	Uncertain significance (Feb 23, 2023)
15-75289430-C-T		not specified	Uncertain significance (Apr 23, 2024)
15-75289452-A-G		not specified	Uncertain significance (Jul 13, 2021)
15-75289454-C-T		not specified	Uncertain significance (Jun 29, 2023)
15-75289610-C-G		not specified	Uncertain significance (Aug 12, 2024)
15-75289628-G-C		not specified	Uncertain significance (Jan 29, 2024)
15-75289631-G-A		not specified	Uncertain significance (May 16, 2022)
15-75289661-G-C		not specified	Uncertain significance (Jan 07, 2025)
15-75289667-T-C		not specified	Uncertain significance (Nov 18, 2022)
15-75293109-A-G		not specified	Uncertain significance (Jan 29, 2025)
15-75293124-C-T		not specified	Likely benign (Nov 09, 2021)
15-75293144-C-G		not specified	Uncertain significance (Feb 12, 2025)
15-75293154-G-A		not specified	Uncertain significance (Dec 19, 2022)
15-75293163-C-T		not specified	Likely benign (Dec 07, 2021)
15-75293729-A-T		not specified	Uncertain significance (Dec 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLGA6D	protein_coding	protein_coding	ENST00000434739	18	11641

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.16e-8	0.0503	123678	1	85	123764	0.000347

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.796	102	81.8	1.25	0.00000480	4448
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00402	0.00390
East Asian	0.000111	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000325	0.000310
Middle Eastern	0.000111	0.000109
South Asian	0.0000344	0.0000327
Other	0.000687	0.000661

dbNSFP

Source: dbNSFP

Haploinsufficiency Scores

• pHI: 0.0696
• hipred: N
• hipred_score: 0.187
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0886

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