ARV1

ARV1 homolog, fatty acid homeostasis modulator

Basic information

Region (hg38): 1:230978980-231000733

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.

• not provided (21 variants)
• Developmental and epileptic encephalopathy, 38 (14 variants)
• Inborn genetic diseases (10 variants)
• Abnormality of the nervous system (1 variants)
• not specified (1 variants)
• ARV1-related condition (1 variants)
• Neurodegeneration;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.

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				3	1	4
missense		1	12	4	1	18
nonsense						0
start loss		1				1
frameshift	1	7				8
inframe indel						0
splice donor/acceptor (+/-2bp)	2	2	2			6
splice region			1			1
non coding				1	1	2
Total	3	11	14	8	3

Highest pathogenic variant AF is 0.0000198

Variants in ARV1

This is a list of pathogenic ClinVar variants found in the ARV1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-230979107-T-C			Likely pathogenic (Jan 30, 2022)
1-230979114-C-T		ARV1-related disorder	Likely benign (Sep 06, 2019)
1-230979134-A-G		Developmental and epileptic encephalopathy, 38	Uncertain significance (Oct 15, 2018)
1-230979154-G-A		Inborn genetic diseases	Uncertain significance (Jun 29, 2023)
1-230979169-A-T		not specified • ARV1-related disorder	Benign/Likely benign (Mar 01, 2024)
1-230979178-G-T		ARV1-related disorder	Likely benign (Oct 01, 2023)
1-230979186-G-T			Likely benign (Jun 01, 2022)
1-230979199-T-C			Benign/Likely benign (Dec 31, 2019)
1-230979206-G-A		Developmental and epileptic encephalopathy, 38	Uncertain significance (Aug 03, 2020)
1-230979230-A-G		Inborn genetic diseases	Uncertain significance (Sep 20, 2023)
1-230979251-AC-A		Inborn genetic diseases	Pathogenic (Feb 08, 2023)
1-230988309-T-C		Developmental and epileptic encephalopathy, 38	Benign (Jul 14, 2021)
1-230988310-A-C			Likely benign (Apr 03, 2018)
1-230988317-CA-TG		Developmental and epileptic encephalopathy, 38	Pathogenic (Dec 16, 2020)
1-230988318-A-G		Developmental and epileptic encephalopathy, 38	Likely pathogenic (Mar 31, 2022)
1-230988324-C-A		Inborn genetic diseases	Uncertain significance (Mar 01, 2024)
1-230988359-G-A			Uncertain significance (Aug 01, 2022)
1-230988362-C-T		Inborn genetic diseases	Uncertain significance (May 26, 2023)
1-230988436-AAATG-A		Developmental and epileptic encephalopathy, 38	Uncertain significance (Jan 01, 2019)
1-230988440-G-A		Developmental and epileptic encephalopathy, 38 • ARV1-related disorder	Pathogenic (Feb 13, 2015)
1-230990105-A-G			Uncertain significance (Jan 01, 2023)
1-230990117-G-A		ARV1-related disorder	Benign (Dec 31, 2019)
1-230990121-ACT-A			Likely pathogenic (Feb 01, 2021)
1-230990169-G-C		Inborn genetic diseases	Uncertain significance (Oct 13, 2023)
1-230990175-A-G			Likely benign (Dec 20, 2017)

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