GOLT1A

protein-coding

golgi transport 1A

Gene summary

Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in Golgi apparatus; endoplasmic reticulum; and nuclear envelope. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_198447.2

Inheritance

—

ClinVar variants

U:26B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.27

Max pathogenic AF

—

Genomic locus

chr1:204,198,163-204,213,988

External References & Databases

Ensembl (ENSG00000174567)

Transcript & Mutation Effects

hg38 • Region Span ~15.8 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 GOLT1A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198447.2. 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				2 clinvar	1 clinvar	3
missense			24 clinvar	3 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	26	5	1	32

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198447.2	RefSeq	NP_940849.1	5	MANE Select
ENST00000308302.4	Ensembl	ENSP00000308535.3	5	MANE Select
ENST00000874691.1	Ensembl	ENSP00000544750.1	5	Standard
ENST00000874691.2	Ensembl	ENSP00000544750.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endoplasmic reticulum to Golgi vesicle-mediated transport
biological_process
protein transport

Molecular Function

molecular_function

Cellular Component

Golgi cis cisterna
Golgi membrane
nuclear envelope
endoplasmic reticulum
trans-Golgi network

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000308302
Coding exons: 5
Length: 15933
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125746
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.597	64	78.9	0.811	0.00000476	851
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00038	0.00038	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000079	0.000079	rare
South Asian	0.000036	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.532

Gene Damage Prediction

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