SMPX small muscle protein X-linked [Homo sapiens (human)] - Gene

Summary

Official Symbol: SMPXprovided by HGNC
Official Full Name: small muscle protein X-linkedprovided by HGNC
Primary source: HGNC:HGNC:11122
See related: Ensembl:ENSG00000091482 MIM:300226; AllianceGenome:HGNC:11122
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: Csl; DFN6; MPD7; DFNX4; Chisel
Summary: This gene encodes a small protein that has no known functional domains. Mutations in this gene are a cause of X-linked deafness-4, and the encoded protein may play a role in the maintenance of inner ear cells subjected to mechanical stress. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2011]
Expression: Restricted expression toward heart (RPKM 174.8) See more
Orthologs: mouse all
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Genomic context

Location:: Xp22.12

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	X	NC_000023.11 (21705978..21758116, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	X	NC_060947.1 (21289285..21341420, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	X	NC_000023.10 (21724096..21776234, complement)

Chromosome X - NC_000023.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

Missense mutations in small muscle protein X-linked (SMPX) cause distal myopathy with protein inclusions.
Title: Missense mutations in small muscle protein X-linked (SMPX) cause distal myopathy with protein inclusions.
In silico analysis of nonsynonymous single-nucleotide polymorphisms (nsSNPs) of the SMPX gene.
Title: In silico analysis of nonsynonymous single-nucleotide polymorphisms (nsSNPs) of the SMPX gene.
A donor splice-site variant in SMPX causes rare X-linked congenital deafness.
Title: Whole-exome sequencing identifies a donor splice-site variant in SMPX that causes rare X-linked congenital deafness.
detected a single nucleotide variation in two male controls with normal hearing, SMPX c.55A>G (p.Asn19Asp), which has been annotated as a rare variant in the Single Nucleotide Polymorphism (dbSNP) (rs759552778) and Exome Aggregation Consortium (ExAC) databases. This study has enriched the mutation spectrum of the SMPX gene
Title: A novel mutation in the SMPX gene associated with X-linked nonsyndromic sensorineural hearing loss in a Chinese family.
Results show that SMPX expression is regulated by NOR-1 which binds to SMPX promoter and induces its activity promoting myotube differentiation.
Title: The nuclear receptor NOR-1 regulates the small muscle protein, X-linked (SMPX) and myotube differentiation.
We report the first SMPX (DFNX4) mutation in a North American family. Our findings contribute to the existing genotypic and phenotypic spectrum of SMPX associated hearing loss. Furthermore, our data suggest that exome sequencing is promising in the genetic diagnosis of hearing loss
Title: A novel splicing mutation in SMPX is linked to nonsyndromic progressive hearing loss.
A novel frameshift mutation in SMPX.
Title: A novel frameshift mutation of SMPX causes a rare form of X-linked nonsyndromic hearing loss in a Chinese family.
Audiological, medical, and family histories were collected and family members interviewed to compare hearing thresholds and case histories between cases with mutations in SMPX versus POU3F4.
Title: X-linked hearing loss: two gene mutation examples provide generalizable implications for clinical care.
SMPX is localized predominantly in repetitive double stripes flanking the Z-disc, and not present in nuclei.
Title: Overexpression of SMPX in adult skeletal muscle does not change skeletal muscle fiber type or size.
Data indicate founder mutation in exon 3 (c.99delC) of SMPX that cosegregates in two Newfoundland families.
Title: A novel deletion in SMPX causes a rare form of X-linked progressive hearing loss in two families due to a founder effect.

Submit: New GeneRIF Correction See all GeneRIFs (13)

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
Hearing loss, X-linked 4 MedGen: C1848204 OMIM: 300066 GeneReviews: Genetic Hearing Loss Overview	Compare labs
Hereditary hearing loss and deafness MedGen: C0236038 GeneReviews: Genetic Hearing Loss Overview	Compare labs
Myopathy, distal, 7, adult-onset, X-linked MedGen: C5676880 OMIM: 301075 GeneReviews: Not available	Compare labs

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

RH41821 (e-PCR)
- UniSTS:17931

DXS8331 (e-PCR)
- UniSTS:21774

DXS365 (e-PCR)
- UniSTS:99625

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in striated muscle contraction	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in M band	IBA Inferred from Biological aspect of Ancestor more info
is_active_in costamere	IBA Inferred from Biological aspect of Ancestor more info
is_active_in muscle tendon junction	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: small muscular protein

Names: deafness, X-linked 6, sensorineural; stretch-responsive skeletal muscle 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_031916.1 RefSeqGene

Range

5045..57183

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1358

mRNA and Protein(s)

NM_014332.3 → NP_055147.1 small muscular protein

See identical proteins and their annotated locations for NP_055147.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and is protein-coding.

Source sequence(s)

AF129505, AK312134

Consensus CDS

CCDS14200.1

UniProtKB/Swiss-Prot

B1AWX2, Q9UHP9

Related

ENSP00000368808.3, ENST00000379494.4

Conserved Domains (1) summary

pfam15355
Location:3 → 87

Chisel; Stretch-responsive small skeletal muscle X protein, Chisel

RNA

NR_045617.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK312134, AL772370, BF126275, BM674432