GOLT1A

golgi transport 1A

Basic information

Region (hg38): 1:204198163-204213988

Links

ENSG00000174567 ∙ NCBI:127845 ∙ ∙ HGNC:24766 ∙ Uniprot:Q6ZVE7 ∙ 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 GOLT1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLT1A 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				1	1	2
missense			12	1		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	2	1

Variants in GOLT1A

This is a list of pathogenic ClinVar variants found in the GOLT1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-204198471-C-T		not specified	Uncertain significance (Dec 19, 2022)
1-204198489-C-T		not specified	Likely benign (May 27, 2022)
1-204199209-G-C		not specified	Uncertain significance (Sep 14, 2022)
1-204201634-T-G		not specified	Uncertain significance (Aug 30, 2021)
1-204201637-A-T		not specified	Uncertain significance (Jun 05, 2024)
1-204201648-A-C		not specified	Uncertain significance (Jun 29, 2023)
1-204201668-C-G		not specified	Uncertain significance (Jul 31, 2024)
1-204201681-G-A		not specified	Uncertain significance (Jul 31, 2024)
1-204201745-G-T			Benign (May 08, 2018)
1-204201759-C-A		not specified	Uncertain significance (Dec 05, 2024)
1-204201798-G-A		not specified	Uncertain significance (Jan 24, 2023)
1-204202916-C-T		not specified	Uncertain significance (Nov 11, 2024)
1-204202941-A-G			Likely benign (Mar 01, 2023)
1-204202960-C-T		not specified	Uncertain significance (Jan 17, 2025)
1-204202967-C-T		not specified	Uncertain significance (Aug 02, 2022)
1-204202970-T-C		not specified	Uncertain significance (Nov 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLT1A	protein_coding	protein_coding	ENST00000308302	5	15933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.237	0.734	125727	0	19	125746	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.597	64	78.9	0.811	0.00000476	851
Missense in Polyphen		27	32.083	0.84157		362
Synonymous	0.891	27	33.6	0.804	0.00000203	273
Loss of Function	1.83	2	7.34	0.272	4.12e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.000381	0.000381
South Asian	0.0000364	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in fusion of ER-derived transport vesicles with the Golgi complex. {ECO:0000269|PubMed:10406798}.

Recessive Scores

• pRec: 0.599

Intolerance Scores

• loftool: 0.559
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.114
• hipred: N
• hipred_score: 0.289
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.532

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golt1a

Gene ontology

• Biological process: endoplasmic reticulum to Golgi vesicle-mediated transport;biological_process;protein transport
• Cellular component: Golgi cis cisterna;Golgi membrane;nuclear envelope;endoplasmic reticulum;trans-Golgi network;integral component of membrane
• Molecular function: molecular_function