SHROOM2 shroom family member 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SHROOM2provided by HGNC
Official Full Name: shroom family member 2provided by HGNC
Primary source: HGNC:HGNC:630
See related: Ensembl:ENSG00000146950 MIM:300103; AllianceGenome:HGNC:630
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: APXL; HSAPXL
Summary: This gene represents the human homolog of Xenopus laevis apical protein (APX) gene, which is implicated in amiloride-sensitive sodium channel activity. It is expressed in endothelial cells and facilitates the formation of a contractile network within endothelial cells. Depletion of this gene results in an increase in endothelial sprouting, migration, and angiogenesis. This gene is highly expressed in the retina, and is a strong candidate for ocular albinism type 1 syndrome. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2016]
Expression: Broad expression in ovary (RPKM 2.6), placenta (RPKM 2.6) and 21 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: Xp22.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (9786429..9949443)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (9369053..9532050)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (9754469..9917483)

Chromosome X - NC_000023.11 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?

SHROOM2 is downregulated in nasopharyngeal carcinoma and is implicated in the suppression of cancer cell invasion and metastasis by preventing EMT, which is largely independent of Rho-ROCK signaling.
Title: SHROOM2 inhibits tumor metastasis through RhoA-ROCK pathway-dependent and -independent mechanisms in nasopharyngeal carcinoma.
SHROOM2 deletion is associated with Ocular albinism with infertility and late-onset sensorineural hearing loss.
Title: Ocular albinism with infertility and late-onset sensorineural hearing loss.
These findings provide genetic and molecular insights into the effects of rare damaging variants in SHROOM2, indicating that such variants of SHROOM2 might contribute to the risk of human Neural tube defects
Title: Genetic and functional analysis of SHROOM1-4 in a Chinese neural tube defect cohort.
We identified three new CRC risk loci at 6p21 (rs1321311, near CDKN1A; P = 1.14 x 10(-10)), 11q13.4 (rs3824999, intronic to POLD3; P = 3.65 x 10(-10)) and Xp22.2 (rs5934683, near SHROOM2; P = 7.30 x 10(-10)).
Title: Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk.
Data suggest that Shroom2 facilitates the formation of a contractile network within endothelial cells, the loss of which leads to an increase in endothelial sprouting, migration, and angiogenesis.
Title: Shroom2 regulates contractility to control endothelial morphogenesis.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk. EBI GWAS Catalog EBI GWAS CatalogPubMed
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array. 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

RH18181 (e-PCR)
- UniSTS:6455

G49443 (e-PCR)
- UniSTS:109186

AF003658 (e-PCR)
- UniSTS:94597

SHGC-58453 (e-PCR)
- UniSTS:94342

AF003664 (e-PCR)
- UniSTS:94603

SHROOM2 (e-PCR)
- UniSTS:506511

GDB:597633 (e-PCR)
- UniSTS:158104

GDB:597645 (e-PCR)
- UniSTS:158105

GDB:597735 (e-PCR)
- UniSTS:158107

GDB:599051 (e-PCR)
- UniSTS:158108

GDB:599415 (e-PCR)
- UniSTS:158145

GDB:599441 (e-PCR)
- UniSTS:158152

GDB:599465 (e-PCR)
- UniSTS:158158

GDB:599475 (e-PCR)
- UniSTS:158160

GDB:599486 (e-PCR)
- UniSTS:158161

GDB:599499 (e-PCR)
- UniSTS:158164

GDB:599508 (e-PCR)
- UniSTS:158165

GDB:599514 (e-PCR)
- UniSTS:158166

GDB:599521 (e-PCR)
- UniSTS:158167

GDB:599525 (e-PCR)
- UniSTS:158168

GDB:599536 (e-PCR)
- UniSTS:158170

GDB:599539 (e-PCR)
- UniSTS:158171

GDB:599542 (e-PCR)
- UniSTS:158172

GDB:599551 (e-PCR)
- UniSTS:158174

GDB:599554 (e-PCR)
- UniSTS:158175

GDB:603613 (e-PCR)
- UniSTS:158180

GDB:603624 (e-PCR)
- UniSTS:158182

GDB:603627 (e-PCR)
- UniSTS:158183

GDB:603631 (e-PCR)
- UniSTS:158184

A007I24 (e-PCR)
- UniSTS:79357

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables actin binding	ISS Inferred from Sequence or Structural Similarity more info
enables actin filament binding	IBA Inferred from Biological aspect of Ancestor more info
enables actin filament binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables beta-catenin binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables ligand-gated sodium channel activity	TAS Traceable Author Statement more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
NOT involved_in actin filament bundle assembly	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in actin filament organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in apical protein localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in brain development	ISS Inferred from Sequence or Structural Similarity more info
involved_in camera-type eye development	ISS Inferred from Sequence or Structural Similarity more info
involved_in camera-type eye morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in cell migration	ISS Inferred from Sequence or Structural Similarity more info
NOT involved_in cell morphogenesis	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in cell morphogenesis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in cellular pigment accumulation	ISS Inferred from Sequence or Structural Similarity more info
involved_in ear development	ISS Inferred from Sequence or Structural Similarity more info
involved_in establishment of melanosome localization	ISS Inferred from Sequence or Structural Similarity more info
involved_in eye pigment granule organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in lens morphogenesis in camera-type eye	ISS Inferred from Sequence or Structural Similarity more info
involved_in melanosome organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in adherens junction	IBA Inferred from Biological aspect of Ancestor more info
located_in adherens junction	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in apical junction complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in apical plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in apical plasma membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in bicellular tight junction	ISS Inferred from Sequence or Structural Similarity more info
colocalizes_with cortical actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
colocalizes_with cortical actin cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular exosome	HDA more info	PubMed
located_in microtubule	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: protein Shroom2

Names: APX homolog of Xenopus; apical-like 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_012493.2 RefSeqGene

Range

4974..167988

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001320663.2 → NP_001307592.1 protein Shroom2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate promoter and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (2) has a shorter N-terminus compared to isoform 1.

Source sequence(s)

AK299907, BC140866, BM678914, X83543

UniProtKB/TrEMBL

Q68DU3

Conserved Domains (1) summary

pfam08687
Location:153 → 444

ASD2; Apx/Shroom domain ASD2
NM_001320664.2 → NP_001307593.1 protein Shroom2 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate promoter, has an alternate in-frame acceptor splice site at the penultimate exon, and initiates translation from an in-frame downstream start codon compared to variant 1. The resulting isoform (3) has a shorter N-terminus and lacks an internal amino acid compared to isoform 1.

Source sequence(s)

AK299907, BC140866, BM678914, CR749271, X83543

Consensus CDS

CCDS83453.1

UniProtKB/TrEMBL

F5H3B6, Q68DU3

Related

ENSP00000415229.3, ENST00000418909.6

Conserved Domains (1) summary

pfam08687
Location:153 → 443

ASD2; Apx/Shroom domain ASD2
NM_001649.4 → NP_001640.1 protein Shroom2 isoform 1

See identical proteins and their annotated locations for NP_001640.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC090481, BC140866, BM678914, X83543

Consensus CDS

CCDS14135.1

UniProtKB/Swiss-Prot

B9EIQ7, Q13796

Related

ENSP00000370299.3, ENST00000380913.8

Conserved Domains (3) summary

cd00992
Location:25 → 105

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam08687
Location:1318 → 1609

ASD2; Apx/Shroom domain ASD2

pfam08688
Location:640 → 802

ASD1; Apx/Shroom domain ASD1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000023.11 Reference GRCh38.p14 Primary Assembly

Range

9786429..9949443

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005274500.5 → XP_005274557.2 protein Shroom2 isoform X1

Conserved Domains (3) summary

cd00992
Location:25 → 105

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

pfam08687
Location:1318 → 1608

ASD2; Apx/Shroom domain ASD2

pfam08688
Location:640 → 802

ASD1; Apx/Shroom domain ASD1
XM_011545506.1 → XP_011543808.1 protein Shroom2 isoform X3

UniProtKB/TrEMBL

Q68DU3

Related

ENSP00000406724.1, ENST00000452575.1

Conserved Domains (1) summary

pfam08687
Location:153 → 444

ASD2; Apx/Shroom domain ASD2
XM_017029492.1 → XP_016884981.1 protein Shroom2 isoform X2

UniProtKB/TrEMBL

F5H3B6, Q68DU3

Conserved Domains (1) summary

pfam08687
Location:153 → 443

ASD2; Apx/Shroom domain ASD2