ASPSCR1

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

Basic information

Region (hg38): 17:81976806-82017406

Links

ENSG00000169696 ∙ NCBI:79058 ∙ OMIM:606236 ∙ HGNC:13825 ∙ Uniprot:Q9BZE9 ∙ 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 ASPSCR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ASPSCR1 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			38	4		42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			3			3
Total	0	0	41	4	0

Variants in ASPSCR1

This is a list of pathogenic ClinVar variants found in the ASPSCR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81977672-G-A		not specified	Uncertain significance (Jul 05, 2023)
17-81977698-A-G		not specified	Uncertain significance (Jan 04, 2024)
17-81979197-C-T		not specified	Uncertain significance (Jan 17, 2023)
17-81979202-C-T		not specified	Uncertain significance (Oct 05, 2023)
17-81979203-G-A		not specified	Uncertain significance (Aug 14, 2023)
17-81979209-A-G		not specified	Uncertain significance (Sep 07, 2022)
17-81983582-C-G		not specified	Uncertain significance (Feb 03, 2022)
17-81983627-A-C		not specified	Uncertain significance (Feb 13, 2023)
17-81983629-G-A		not specified	Uncertain significance (Feb 07, 2023)
17-81983630-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-81983640-C-T		not specified	Uncertain significance (Aug 08, 2022)
17-81983642-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-81983649-G-A		not specified	Uncertain significance (Jul 14, 2022)
17-81985511-G-T		not specified	Uncertain significance (May 27, 2022)
17-81985538-C-T		not specified	Uncertain significance (May 14, 2024)
17-81985559-G-T		not specified	Uncertain significance (Aug 28, 2023)
17-81995996-C-T		not specified	Likely benign (Dec 21, 2021)
17-81996014-G-A		not specified	Likely benign (Mar 29, 2022)
17-81996473-C-T		not specified	Uncertain significance (Dec 26, 2023)
17-81996476-C-T		not specified	Uncertain significance (Dec 08, 2023)
17-81996479-C-T		not specified	Likely benign (Apr 26, 2023)
17-81996484-G-C		not specified	Uncertain significance (Jul 08, 2022)
17-81996505-G-A		not specified	Likely benign (Aug 02, 2021)
17-81996538-C-T		not specified	Uncertain significance (Jun 07, 2024)
17-81996544-G-A		not specified	Uncertain significance (Oct 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ASPSCR1	protein_coding	protein_coding	ENST00000306729	17	40600

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.42e-12	0.774	124364	11	1373	125748	0.00552

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.00184	404	404	1.00	0.0000268	4059
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0108	0.0104
Ashkenazi Jewish	0.0172	0.0163
East Asian	0.0000545	0.0000544
Finnish	0.00433	0.00324
European (Non-Finnish)	0.00723	0.00676
Middle Eastern	0.0000545	0.0000544
South Asian	0.00380	0.00353
Other	0.00783	0.00752

dbNSFP

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}.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.439

Intolerance Scores

• loftool: 0.758
• rvis_EVS: -0.69
• rvis_percentile_EVS: 15.32

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.169
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.952

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aspscr1

Gene ontology

• Biological process: intracellular protein transport;positive regulation of protein modification process;glucose homeostasis;regulation of glucose import
• Cellular component: nucleoplasm;cytosol;plasma membrane;cytoplasmic side of plasma membrane;endomembrane system;vesicle membrane;extrinsic component of membrane;endoplasmic reticulum-Golgi intermediate compartment membrane;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: protein binding