USH2A usherin [Homo sapiens (human)] - Gene

Summary

Official Symbol: USH2Aprovided by HGNC
Official Full Name: usherinprovided by HGNC
Primary source: HGNC:HGNC:12601
See related: Ensembl:ENSG00000042781 MIM:608400; AllianceGenome:HGNC:12601
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: US2; RP39; USH2; dJ1111A8.1
Summary: This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
Expression: Biased expression in liver (RPKM 1.7), testis (RPKM 0.3) and 1 other tissue See more
Orthologs: mouse all
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Genomic context

Location:: 1q41

Exon count:: 72

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (215622891..216423448, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (214863291..215663779, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (215796233..216596790, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Functional Vision in Patients With Biallelic USH2A Variants.
Title: Functional Vision in Patients With Biallelic USH2A Variants.
The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes.
Title: The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes.
USH2A variants causing retinitis pigmentosa or Usher syndrome provoke differential retinal phenotypes in disease-specific organoids.
Title: USH2A variants causing retinitis pigmentosa or Usher syndrome provoke differential retinal phenotypes in disease-specific organoids.
Expression of the human usherin c.2299delG mutation leads to early-onset auditory loss and stereocilia disorganization.
Title: Expression of the human usherin c.2299delG mutation leads to early-onset auditory loss and stereocilia disorganization.
Change in Cone Structure Over 24 Months in USH2A-Related Retinal Degeneration.
Title: Change in Cone Structure Over 24 Months in USH2A-Related Retinal Degeneration.
USH2A mutational spectrum causing syndromic and non-syndromic retinal dystrophies in a large cohort of Mexican patients.
Title: USH2A mutational spectrum causing syndromic and non-syndromic retinal dystrophies in a large cohort of Mexican patients.
Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction.
Title: Whole genome sequencing for USH2A-associated disease reveals several pathogenic deep-intronic variants that are amenable to splice correction.
Natural Disease Course in Usher Syndrome Patients Harboring USH2A Variant p.Cys870* in Exon 13, Amenable to Exon Skipping Therapy.
Title: Natural Disease Course in Usher Syndrome Patients Harboring USH2A Variant p.Cys870* in Exon 13, Amenable to Exon Skipping Therapy.
Exome sequencing identified five novel USH2A variants in Korean patients with retinitis pigmentosa.
Title: Exome sequencing identified five novel USH2A variants in Korean patients with retinitis pigmentosa.
Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review.
Title: Characterizing the genotypic spectrum of retinitis pigmentosa in East Asian populations: a systematic review.

Submit: New GeneRIF Correction See all GeneRIFs (119)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Retinitis pigmentosa 39 MedGen: C3151138 OMIM: 613809 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview	Compare labs
Usher syndrome type 2A MedGen: C1848634 OMIM: 276901 GeneReviews: Usher Syndrome Type II	Compare labs

EBI GWAS Catalog

Description
Dissecting the genetics of chronic mucus hypersecretion in smokers with and without COPD. EBI GWAS Catalog EBI GWAS CatalogPubMed
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL009851 (e-PCR)
- UniSTS:41728

SHGC-132295 (e-PCR)
- UniSTS:170766

G63076 (e-PCR)
- UniSTS:140051

G62491 (e-PCR)
- UniSTS:139549

SHGC-78958 (e-PCR)
- UniSTS:100906

D1S2827 (e-PCR), detects polymorphism
- UniSTS:50739

SHGC-155213 (e-PCR)
- UniSTS:182068

AL009345 (e-PCR)
- UniSTS:13111

SHGC-106817 (e-PCR)
- UniSTS:170049

AL033887 (e-PCR)
- UniSTS:93763

AL010107 (e-PCR)
- UniSTS:9033

SHGC-84884 (e-PCR)
- UniSTS:104780

AL034204 (e-PCR)
- UniSTS:94030

D1S2171 (e-PCR)
- UniSTS:50772

AFM248tc1 (e-PCR)
- UniSTS:36951

AL009491 (e-PCR)
- UniSTS:61537

RH79627 (e-PCR)
- UniSTS:90212

RH118881 (e-PCR)
- UniSTS:138861

D1S2435 (e-PCR)
- UniSTS:67214

SHGC-111484 (e-PCR)
- UniSTS:181917

AL009855 (e-PCR)
- UniSTS:23467

AL009286 (e-PCR)
- UniSTS:32686

AL033963 (e-PCR)
- UniSTS:93375

D1S2086 (e-PCR)
- UniSTS:35009

AL034147 (e-PCR)
- UniSTS:93917

SHGC-76355 (e-PCR)
- UniSTS:78303

143XF10 (e-PCR)
- UniSTS:6625

RH119862 (e-PCR)
- UniSTS:133607

SHGC-144902 (e-PCR)
- UniSTS:174316

AFM268zd1 (e-PCR)
- UniSTS:52214

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables collagen binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables myosin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in hair cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear auditory receptor cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in inner ear receptor cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in inner ear receptor cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in maintenance of animal organ identity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of USH2 complex	ISS Inferred from Sequence or Structural Similarity more info
located_in apical plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in basement membrane	IDA Inferred from Direct Assay more info	PubMed
located_in ciliary basal body	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in extracellular region	IEA Inferred from Electronic Annotation more info
colocalizes_with neuronal cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in periciliary membrane compartment	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with photoreceptor connecting cilium	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with photoreceptor inner segment	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilia ankle link	ISS Inferred from Sequence or Structural Similarity more info
part_of stereocilia ankle link complex	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium bundle	ISS Inferred from Sequence or Structural Similarity more info
located_in stereocilium membrane	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with terminal bouton	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: usherin

Names: Usher syndrome 2A (autosomal recessive, mild); usher syndrome type IIa protein; usher syndrome type-2A protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_009497.2 RefSeqGene

Range

5001..805558

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_007123.6 → NP_009054.6 usherin isoform A precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) uses a different splice site in its 3' coding region when compared to variant 2. The resulting protein (isoform A) has a shorter and distinct C-terminus, compared to isoform B.

Source sequence(s)

AC138024, AF055580, AL358858, AL445650

Consensus CDS

CCDS1516.1

Related

ENSP00000355909.3, ENST00000366942.3

Conserved Domains (8) summary

smart00060
Location:1368 → 1451

FN3; Fibronectin type 3 domain

smart00180
Location:847 → 897

EGF_Lam; Laminin-type epidermal growth factor-like domai

smart00560
Location:146 → 283

LamGL; LamG-like jellyroll fold domain

cd00055
Location:900 → 948

EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...

cd00063
Location:1242 → 1357

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

pfam00041
Location:1058 → 1132

fn3; Fibronectin type III domain

pfam00053
Location:641 → 691

Laminin_EGF; Laminin EGF domain

cl02806
Location:291 → 516

Laminin_N; Laminin N-terminal (Domain VI)
NM_206933.4 → NP_996816.3 usherin isoform B precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) is the longer transcript and it encodes the longer isoform (B).

Source sequence(s)

AC092799, AL445650, AY481573

Consensus CDS

CCDS31025.1

UniProtKB/Swiss-Prot

O75445, Q5VVM9, Q6S362, Q9NS27

UniProtKB/TrEMBL

A0A0K1P7S2

Related

ENSP00000305941.3, ENST00000307340.8

Conserved Domains (9) summary

smart00060
Location:1368 → 1451

FN3; Fibronectin type 3 domain

smart00180
Location:847 → 897

EGF_Lam; Laminin-type epidermal growth factor-like domai

smart00560
Location:146 → 283

LamGL; LamG-like jellyroll fold domain

cd00055
Location:900 → 948

EGF_Lam; Laminin-type epidermal growth factor-like domain; laminins are the major noncollagenous components of basement membranes that mediate cell adhesion, growth migration, and differentiation; the laminin-type epidermal growth factor-like module occurs in ...

cd00063
Location:2533 → 2619

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00110
Location:1716 → 1868

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

pfam00041
Location:1150 → 1227

fn3; Fibronectin type III domain

pfam00053
Location:641 → 691

Laminin_EGF; Laminin EGF domain

cl02806
Location:291 → 516

Laminin_N; Laminin N-terminal (Domain VI)