ARRDC1

arrestin domain containing 1, the group of Alpha arrestins

Basic information

Region (hg38): 9:137605684-137615360

Links

ENSG00000197070 ∙ NCBI:92714 ∙ OMIM:619768 ∙ HGNC:28633 ∙ Uniprot:Q8N5I2 ∙ 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 ARRDC1 gene.

• Inborn genetic diseases (40 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARRDC1 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			36	4		40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	4	0

Variants in ARRDC1

This is a list of pathogenic ClinVar variants found in the ARRDC1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137605725-G-T		not specified	Uncertain significance (Jun 13, 2023)
9-137605754-C-T		not specified	Uncertain significance (Feb 24, 2022)
9-137605774-C-A		not specified	Uncertain significance (Jul 19, 2023)
9-137605784-C-T		not specified	Uncertain significance (Feb 16, 2023)
9-137605805-G-A		not specified	Uncertain significance (Feb 13, 2023)
9-137605818-C-T		not specified	Uncertain significance (Jul 12, 2022)
9-137605827-C-T		not specified	Uncertain significance (Nov 10, 2022)
9-137612943-A-C		not specified	Uncertain significance (Jan 18, 2023)
9-137612979-A-T		not specified	Uncertain significance (Jul 25, 2023)
9-137612981-C-G		not specified	Uncertain significance (Dec 15, 2022)
9-137612988-C-G		not specified	Uncertain significance (May 31, 2023)
9-137613615-C-T		not specified	Uncertain significance (Nov 10, 2022)
9-137613624-C-G		not specified	Uncertain significance (Jul 17, 2023)
9-137613642-C-T		not specified	Uncertain significance (Apr 18, 2023)
9-137613690-G-A		not specified	Uncertain significance (Aug 04, 2021)
9-137613726-A-T		not specified	Uncertain significance (Jan 18, 2022)
9-137613737-C-G		not specified	Uncertain significance (Feb 15, 2023)
9-137614092-G-A		not specified	Uncertain significance (Mar 07, 2024)
9-137614102-C-T		not specified	Uncertain significance (Feb 12, 2024)
9-137614120-G-A		not specified	Uncertain significance (Jan 18, 2022)
9-137614125-T-G		not specified	Uncertain significance (May 23, 2023)
9-137614335-G-A		not specified	Uncertain significance (Apr 12, 2023)
9-137614383-C-T		not specified	Uncertain significance (Aug 15, 2023)
9-137614398-G-A		not specified	Uncertain significance (Sep 12, 2023)
9-137614572-C-T		not specified	Likely benign (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARRDC1	protein_coding	protein_coding	ENST00000371421	8	9707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000136	0.625	125686	0	59	125745	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.116	267	262	1.02	0.0000162	2752
Missense in Polyphen		83	84.242	0.98525		898
Synonymous	-0.913	138	125	1.10	0.00000902	948
Loss of Function	0.997	11	15.2	0.724	6.47e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000333	0.000329
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000932	0.0000924
European (Non-Finnish)	0.000297	0.000290
Middle Eastern	0.000163	0.000163
South Asian	0.000332	0.000327
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as an adapter recruiting ubiquitin-protein ligases to their specific substrates (PubMed:23886940, PubMed:27462458). Through an ubiquitination-dependent mechanism plays for instance a role in the incorporation of SLC11A2 into extracellular vesicles (PubMed:27462458). More generally, plays a role in the extracellular transport of proteins between cells through the release in the extracellular space of microvesicles (PubMed:22315426). By participating to the ITCH-mediated ubiquitination and subsequent degradation of NOTCH1, negatively regulates the NOTCH signaling pathway (PubMed:23886940). {ECO:0000269|PubMed:22315426, ECO:0000269|PubMed:23886940, ECO:0000269|PubMed:27462458}.

Intolerance Scores

• loftool: 0.757
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Haploinsufficiency Scores

• pHI: 0.0921
• hipred: Y
• hipred_score: 0.550
• ghis: 0.463

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arrdc1
• Phenotype: cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;extracellular transport;protein transport;protein ubiquitination;negative regulation of Notch signaling pathway;extracellular vesicle biogenesis
• Cellular component: plasma membrane;cytoplasmic vesicle;extracellular exosome;extracellular vesicle
• Molecular function: protein binding;ubiquitin protein ligase binding;identical protein binding;protein binding, bridging involved in substrate recognition for ubiquitination;arrestin family protein binding