GOLT1B

protein-coding

golgi transport 1B

Gene summary

Involved in positive regulation of canonical NF-kappaB signal transduction. Located in endoplasmic reticulum. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016072.5

Inheritance

—

ClinVar variants

U:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr12:21,501,781-21,518,408

External References & Databases

Ensembl (ENSG00000111711)

Transcript & Mutation Effects

hg38 • Region Span ~16.6 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 GOLT1B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016072.5. 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						0
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	13	0	0	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016072.5	RefSeq	NP_057156.1	5	MANE Select
ENST00000229314.10	Ensembl	ENSP00000229314.4	5	MANE Select
ENST00000539025.5	Ensembl	ENSP00000446405.1	3	Standard
ENST00000539663.5	Ensembl	ENSP00000440666.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
vesicle-mediated transport
positive regulation of I-kappaB kinase/NF-kappaB signaling

Cellular Component

Golgi membrane
endoplasmic reticulum
membrane
integral component of membrane
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000229314
Coding exons: 5
Length: 16628
Individuals with no LoFs: 125666
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125669
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.01	44	67.3	0.654	0.00000293	899
Missense (PolyPhen)		18	28.771	0.62564		405
Synonymous	-0.0873	26	25.4	1.02	0.00000129	270
Loss of Function	2.32	0	6.28	0.00	2.61e-7	90

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in fusion of ER-derived transport vesicles with the Golgi complex.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.449
RVIS EVS: 0.5
RVIS percentile EVS: 79.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.404

Gene Damage Prediction

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