GOLT1B

golgi transport 1B

Basic information

Region (hg38): 12:21501781-21518408

Links

ENSG00000111711 ∙ NCBI:51026 ∙ OMIM:615078 ∙ HGNC:20175 ∙ Uniprot:Q9Y3E0 ∙ 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 GOLT1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GOLT1B 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	4	1	0

Variants in GOLT1B

This is a list of pathogenic ClinVar variants found in the GOLT1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-21501800-C-A			Likely benign (Jun 23, 2018)
12-21506914-G-A		not specified	Uncertain significance (Dec 10, 2024)
12-21508410-G-A		not specified	Uncertain significance (Sep 27, 2024)
12-21508457-A-C		not specified	Uncertain significance (Sep 27, 2021)
12-21512374-T-C		not specified	Uncertain significance (Mar 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GOLT1B	protein_coding	protein_coding	ENST00000229314	5	16628

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.853	0.145	125666	0	3	125669	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	44	67.3	0.654	0.00000293	899
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000910	0.0000907
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.203
• hipred: Y
• hipred_score: 0.507

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.404

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Golt1b

Gene ontology

• 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