AUP1

AUP1 lipid droplet regulating VLDL assembly factor

Basic information

Region (hg38): 2:74526645-74529760

Links

ENSG00000115307 ∙ NCBI:550 ∙ OMIM:602434 ∙ HGNC:891 ∙ Uniprot:Q9Y679 ∙ 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 AUP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AUP1 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			1	1	1	3
missense			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			3	3	1	7
Total	0	0	32	5	2

Variants in AUP1

This is a list of pathogenic ClinVar variants found in the AUP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74526972-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-74526987-C-T		not specified	Uncertain significance (Jan 04, 2024)
2-74527313-C-T		not specified	Uncertain significance (May 23, 2023)
2-74527319-C-T		not specified	Uncertain significance (Feb 17, 2024)
2-74527341-C-G		not specified	Uncertain significance (May 02, 2024)
2-74527475-G-T		not specified	Uncertain significance (Mar 31, 2023)
2-74527513-C-T		not specified	Uncertain significance (Apr 20, 2023)
2-74527537-T-C		not specified	Uncertain significance (Oct 18, 2021)
2-74527768-C-T		not specified	Uncertain significance (Jun 06, 2023)
2-74527773-C-T		not specified	Uncertain significance (Apr 25, 2023)
2-74527774-A-T		not specified	Uncertain significance (Jan 29, 2024)
2-74527778-G-A		not specified	Uncertain significance (Sep 14, 2023)
2-74527981-G-C		not specified	Uncertain significance (Nov 03, 2023)
2-74528252-C-T		not specified	Uncertain significance (Mar 06, 2023)
2-74528448-G-A		not specified	Uncertain significance (Jul 05, 2022)
2-74528757-C-T		not specified	Uncertain significance (Apr 07, 2022)
2-74528817-G-C		not specified	Uncertain significance (Dec 26, 2023)
2-74528844-C-A		not specified	Uncertain significance (May 17, 2023)
2-74528874-C-T		not specified	Uncertain significance (Apr 18, 2024)
2-74528877-T-C		not specified	Uncertain significance (Feb 10, 2022)
2-74528920-G-T		not specified	Uncertain significance (Nov 07, 2022)
2-74529115-G-A			Benign (Aug 14, 2018)
2-74529158-C-T		not specified	Uncertain significance (Apr 26, 2024)
2-74529239-G-A		not specified	Uncertain significance (May 30, 2023)
2-74529259-G-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AUP1	protein_coding	protein_coding	ENST00000377526	12	3295

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000160	0.994	124785	0	13	124798	0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.586	212	237	0.893	0.0000129	2595
Missense in Polyphen		70	95.708	0.73139		1061
Synonymous	0.117	93	94.4	0.985	0.00000466	879
Loss of Function	2.41	10	22.3	0.448	0.00000105	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000191	0.000186
European (Non-Finnish)	0.0000537	0.0000530
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the translocation of terminally misfolded proteins from the endoplasmic reticulum lumen to the cytoplasm and their degradation by the proteasome. {ECO:0000269|PubMed:18711132}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.246
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.387
• hipred: Y
• hipred_score: 0.704
• ghis: 0.410

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.823

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Aup1

Gene ontology

• Biological process: ubiquitin-dependent ERAD pathway;retrograde protein transport, ER to cytosol;regulation of catalytic activity
• Cellular component: Hrd1p ubiquitin ligase ERAD-L complex;membrane;integral component of endoplasmic reticulum membrane;extracellular exosome
• Molecular function: protein binding;ubiquitin binding;ubiquitin-protein transferase activator activity