ARV1

ARV1 homolog, fatty acid homeostasis modulator

Basic information

Region (hg38): 1:230978981-231000733

Links

ENSG00000173409 ∙ NCBI:64801 ∙ OMIM:611647 ∙ HGNC:29561 ∙ Uniprot:Q9H2C2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy, 38 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 38	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	25558065; 27270415

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARV1 gene.

• Inborn_genetic_diseases (34 variants)
• not_provided (24 variants)
• Developmental_and_epileptic_encephalopathy,_38 (18 variants)
• ARV1-related_disorder (8 variants)
• not_specified (2 variants)
• 3-methylglutaconic_aciduria,_type_VIIB (2 variants)
• Abnormality_of_the_nervous_system (1 variants)
• Neurodegeneration (1 variants)
• Blindness (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARV1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000022786.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5	1	6
missense		1	37	4	1	43
nonsense						0
start loss		1				1
frameshift	3	7				10
splice donor/acceptor (+/-2bp)	2	3	2			7
Total	5	12	39	9	2

Highest pathogenic variant AF is 0.0000745529

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARV1	protein_coding	protein_coding	ENST00000310256	5	21615

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000359	0.594	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.192	139	146	0.955	0.00000699	1783
Missense in Polyphen		50	52.429	0.95368		700
Synonymous	0.390	54	57.8	0.935	0.00000293	501
Loss of Function	0.886	10	13.5	0.740	5.73e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000178	0.000178
Ashkenazi Jewish	0.000115	0.0000992
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000163	0.000163
South Asian	0.0000660	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role as a mediator in the endoplasmic reticulum (ER) cholesterol and bile acid homeostasis (PubMed:11063737, PubMed:12145310, PubMed:20663892). Participates in sterol transport out of the ER and distribution into plasma membranes (PubMed:20663892). {ECO:0000269|PubMed:11063737, ECO:0000269|PubMed:12145310, ECO:0000269|PubMed:20663892}.
• Pathway: Metabolism of lipids;Metabolism;Metabolism of steroids;Cholesterol biosynthesis (Consensus)

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 0.33
• rvis_percentile_EVS: 73.27

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.216
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.766

Mouse Genome Informatics

• Gene name: Arv1
• Phenotype: growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype

Gene ontology

• Biological process: sphingolipid metabolic process;cholesterol biosynthetic process;bile acid metabolic process;sterol metabolic process;cholesterol transport;intracellular sterol transport;regulation of intracellular cholesterol transport;regulation of cholesterol metabolic process;regulation of plasma membrane sterol distribution
• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane;cortical endoplasmic reticulum
• Molecular function: sterol transporter activity