ARR3

arrestin 3, the group of Classical arrestins

Basic information

Region (hg38): X:70268304-70281840

Links

ENSG00000120500 ∙ NCBI:407 ∙ OMIM:301770 ∙ HGNC:710 ∙ Uniprot:P36575 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myopia 26, X-linked, female-limited (Moderate), mode of inheritance: XL
• myopia 26, X-linked, female-limited (Strong), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopia 26, X-linked, female-limited	XL	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	Ophthalmologic	27829781

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARR3 gene.

• Inborn genetic diseases (11 variants)
• not provided (10 variants)
• Myopia 26, X-linked, female-limited (2 variants)
• ARR3-related condition (2 variants)
• Anophthalmia-microphthalmia syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARR3 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			12	2	2	16
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	1	0	12	5	3

Variants in ARR3

This is a list of pathogenic ClinVar variants found in the ARR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-70269680-C-T		ARR3-related disorder	Benign (Dec 09, 2019)
X-70269896-A-T		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
X-70269910-G-A			Likely benign (Apr 06, 2018)
X-70270102-G-A		ARR3-related disorder	Uncertain significance (May 16, 2023)
X-70270131-A-C		Inborn genetic diseases	Uncertain significance (Jan 17, 2023)
X-70276129-G-T			Pathogenic (Apr 01, 2024)
X-70276150-C-T		Myopia 26, X-linked, female-limited • ARR3-related disorder	Pathogenic (Sep 28, 2023)
X-70276175-T-C		Myopia 26, X-linked, female-limited	Pathogenic (Dec 22, 2017)
X-70276234-C-T		Myopia 26, X-linked, female-limited	Pathogenic (Dec 22, 2017)
X-70276253-G-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
X-70276266-C-A		ARR3-related disorder	Likely pathogenic (Nov 13, 2023)
X-70276429-C-T			Benign (Mar 29, 2018)
X-70276680-T-G		Inborn genetic diseases	Uncertain significance (Aug 28, 2023)
X-70276720-G-A		Inborn genetic diseases	Uncertain significance (Dec 21, 2023)
X-70277417-G-A		Inborn genetic diseases	Uncertain significance (Dec 18, 2023)
X-70277473-C-T		Myopia 26, X-linked, female-limited	Benign (Dec 12, 2023)
X-70277474-G-C		Inborn genetic diseases	Uncertain significance (Mar 29, 2022)
X-70277476-C-T		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
X-70277477-G-A		Inborn genetic diseases	Uncertain significance (Dec 12, 2023)
X-70277494-C-G		Inborn genetic diseases	Uncertain significance (Dec 01, 2022)
X-70277497-C-T			Likely benign (Mar 01, 2023)
X-70277727-C-T			Benign (Mar 29, 2018)
X-70277755-A-G			Likely benign (Nov 01, 2022)
X-70278572-G-A		Inborn genetic diseases	Uncertain significance (Jan 26, 2022)
X-70278580-C-T		Inborn genetic diseases	Uncertain significance (Jul 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARR3	protein_coding	protein_coding	ENST00000307959	16	13536

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.104	0.895	125685	0	5	125690	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.572	131	151	0.869	0.0000119	2507
Missense in Polyphen		37	48.239	0.76701		876
Synonymous	0.411	55	59.0	0.932	0.00000453	774
Loss of Function	2.82	5	17.8	0.280	0.00000141	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000365	0.0000365
Ashkenazi Jewish	0.00	0.00
East Asian	0.000220	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000125	0.00000879
Middle Eastern	0.000220	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in an as yet undefined retina-specific signal transduction. Could binds to photoactivated-phosphorylated red/green opsins.
• Pathway: CXCR4-mediated signaling events;Thromboxane A2 receptor signaling;Visual signal transduction: Cones (Consensus)

Recessive Scores

• pRec: 0.192

Intolerance Scores

• loftool: 0.502
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.662
• hipred: Y
• hipred_score: 0.612
• ghis: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.712

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arr3
• Phenotype: vision/eye phenotype

Zebrafish Information Network

• Gene name: arr3a
• Affected structure: visual perception
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: regulation of protein phosphorylation;endocytosis;signal transduction;visual perception
• Cellular component: photoreceptor outer segment;photoreceptor inner segment;cytoplasm;synapse
• Molecular function: opsin binding;protein binding;phosphoprotein binding