ASPSCR1

protein-coding

ASPSCR1 tether for SLC2A4, UBX domain containing, the group of UBX domain containing

Gene summary

The protein encoded by this gene contains a UBX domain and interacts with glucose transporter type 4 (GLUT4). This protein is a tether, which sequesters the GLUT4 in intracellular vesicles in muscle and fat cells in the absence of insulin, and redistributes the GLUT4 to the plasma membrane within minutes of insulin stimulation. Translocation t(X;17)(p11;q25) of this gene with transcription factor TFE3 gene results in a ASPSCR1-TFE3 fusion protein in alveolar soft part sarcoma and in renal cell carcinomas. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2011]

MANE transcript

NM_024083.4

Inheritance

—

ClinVar variants

U:112B:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr17:81,976,807-82,017,406

External References & Databases

Ensembl (ENSG00000169696)

Transcript & Mutation Effects

hg38 • Region Span ~40.6 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 ASPSCR1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 109

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024083.4. 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			5 clinvar			5
missense			100 clinvar	11 clinvar		111
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	112	11	0	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024083.4	RefSeq	NP_076988.1	16	MANE Select
ENST00000306739.9	Ensembl	ENSP00000302176.4	16	MANE Select
NM_001251888.2	RefSeq	NP_001238817.1	17	Standard
NM_001330528.2	RefSeq	NP_001317457.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transcriptional misregulation in cancer - Homo sapiens (human)

Biological Process

intracellular protein transport
positive regulation of protein modification process
glucose homeostasis
regulation of glucose import

Molecular Function

protein binding

Cellular Component

nucleoplasm
cytosol
plasma membrane
cytoplasmic side of plasma membrane
endomembrane system

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000306729
Coding exons: 17
Length: 40600
Individuals with no LoFs: 124364
Homozygous LoFs: 11
Heterozygous LoFs: 1373
Defined: 125748
p: 0.00552

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.00184	404	404	1.00	0.0000268	4059
Missense (PolyPhen)		68	68.34	0.99503		707
Synonymous	-0.770	194	181	1.07	0.0000130	1383
Loss of Function	1.71	23	33.7	0.682	0.00000178	367

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0073	0.0069	notable
Latino/Admixed American	0.0035	0.0034	notable
Ashkenazi Jewish	0.017	0.016	notable
East Asian	0.000054	0.000054	rare
Finnish	0.0043	0.0032	notable
European (Non-Finnish)	0.0072	0.0068	notable
South Asian	0.0038	0.0035	notable
Other	0.0078	0.0075	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Tethering protein that sequesters GLUT4-containing vesicles in the cytoplasm in the absence of insulin. Modulates the amount of GLUT4 that is available at the cell surface (By similarity). Enhances VCP methylation catalyzed by VCPKMT. {ECO:0000250, ECO:0000269|PubMed:23349634}.;
Disease: DISEASE: Note=A chromosomal aberration involving ASPSCR1 has been found in two patients with of papillary renal cell carcinoma. Translocation t(X;17)(p11.2;q25). {ECO:0000269|PubMed:11358836}.;

Recessive Scores

pRec: 0.439

Intolerance Scores

LoFtool: 0.758
RVIS EVS: -0.69
RVIS percentile EVS: 15.32

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.952

Gene Damage Prediction

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