TRARG1

trafficking regulator of GLUT4 (SLC2A4) 1, the group of interferon induced transmembrane protein domain containing

Basic information

Region (hg38): 17:1279662-1300978

Previous symbols: [ "TUSC5" ]

Links

ENSG00000184811 ∙ NCBI:286753 ∙ OMIM:612211 ∙ HGNC:29592 ∙ Uniprot:Q8IXB3 ∙ 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 TRARG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRARG1 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			12	3		15
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	3	0

Variants in TRARG1

This is a list of pathogenic ClinVar variants found in the TRARG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1280006-C-G		not specified	Uncertain significance (Dec 11, 2023)
17-1280093-C-T		not specified	Uncertain significance (Dec 14, 2023)
17-1280116-A-G		not specified	Uncertain significance (Jul 11, 2023)
17-1280144-C-T		not specified	Uncertain significance (May 14, 2024)
17-1280240-G-A		not specified	Uncertain significance (Mar 29, 2022)
17-1280258-C-T		not specified	Uncertain significance (Mar 31, 2022)
17-1280347-G-T		not specified	Uncertain significance (Dec 18, 2023)
17-1280360-A-G		not specified	Uncertain significance (Mar 04, 2024)
17-1280387-T-C		not specified	Uncertain significance (Apr 22, 2022)
17-1295502-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-1295551-C-T		not specified	Uncertain significance (Dec 13, 2022)
17-1295573-T-C		not specified	Uncertain significance (Feb 06, 2023)
17-1295587-G-A		not specified	Likely benign (Sep 07, 2022)
17-1295596-A-G		not specified	Uncertain significance (Jun 24, 2022)
17-1295597-T-C		not specified	Likely benign (Nov 17, 2023)
17-1295598-G-A		not specified	Likely benign (Aug 01, 2023)
17-1295605-G-A		not specified	Uncertain significance (Apr 16, 2024)
17-1298257-A-G		not specified	Uncertain significance (Apr 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRARG1	protein_coding	protein_coding	ENST00000333813	3	21325

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000524	0.470	124782	0	11	124793	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.437	129	116	1.11	0.00000736	1125
Missense in Polyphen		40	39.792	1.0052		401
Synonymous	-1.13	66	55.3	1.19	0.00000400	392
Loss of Function	0.166	5	5.42	0.923	2.31e-7	60

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.0000482	0.0000464
European (Non-Finnish)	0.0000178	0.0000177
Middle Eastern	0.000112	0.000111
South Asian	0.0000658	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates insulin-mediated adipose tissue glucose uptake and transport by modulation of SLC2A4 recycling. Not required for SLC2A4 membrane fusion upon an initial stimulus, but rather is necessary for proper protein recycling during prolonged insulin stimulation. {ECO:0000250|UniProtKB:Q8C838}.

Intolerance Scores

• rvis_EVS: 1.26
• rvis_percentile_EVS: 93.53

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180
• ghis: 0.396

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Trarg1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: trarg1a
• Affected structure: Rohon-Beard neuron
• Phenotype tag: abnormal
• Phenotype quality: loose

Gene ontology

• Biological process: cellular response to insulin stimulus;glucose import in response to insulin stimulus;protein localization to plasma membrane;vesicle fusion to plasma membrane;endosome to plasma membrane protein transport
• Cellular component: plasma membrane;endomembrane system;membrane;integral component of membrane;cytoplasmic vesicle membrane;perinuclear region of cytoplasm