SMPX (small muscle protein X-linked)

Gene

• Entrez ID: 23676
• Gene name: Small muscle protein X-linked
• Gene symbol: SMPX
• Synonyms (NCBI Gene): Chisel, Csl, DFN6, DFNX4, MPD7
• Chromosome: X
• Chromosome location: Xp22.12
• 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs387906706	C>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs387906707	C>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs387906708	C>A	Pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs398122848	C>-	Pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs398122930	G>-,GG	Likely-pathogenic, pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1060499590	C>T	Likely-pathogenic	Splice acceptor variant
rs1569308571	->T	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT2111374	hsa-miR-1972	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005927	Component	Muscle tendon junction	IBA
GO:0005927	Component	Muscle tendon junction	IEA
GO:0006941	Process	Striated muscle contraction	TAS	10598820
GO:0031430	Component	M band	IBA
GO:0031430	Component	M band	IEA
GO:0043034	Component	Costamere	IBA
GO:0043034	Component	Costamere	IEA
GO:0043292	Component	Contractile muscle fiber	IEA

Other IDs

• MIM: 300226
• HGNC: 11122
• e!Ensembl: ENSG00000091482

Protein

• UniProt ID: Q9UHP9
• Protein name: Small muscular protein (Stretch-responsive skeletal muscle protein)
• Protein function: Plays a role in the regulatory network through which muscle cells coordinate their structural and functional states during growth, adaptation, and repair.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15355	Chisel	3 → 87	Stretch-responsive small skeletal muscle X protein, Chisel	Family

• Tissue specificity: TISSUE SPECIFICITY: Preferentially and abundantly expressed in heart and skeletal muscle.
• Sequence:

  MNMSKQPVSNVRAIQANINIPMGAFRPGAGQPPRRKECTPEVEEGVPPTSDEEKKPIPGA
  KKLPGPAVNLSEIQNIKSELKYVPKAEQ

• Sequence length: 88

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Hearing impairment	Likely pathogenic	rs2147387122	RCV001375371	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hearing loss, X-linked 4	Likely pathogenic; Pathogenic	rs2147390444, rs2519503836, rs387906706, rs387906707, rs387906708, rs398122848, rs1060499590, rs398122930, rs2092830420	RCV002051748 RCV003881672 RCV000022837 RCV000022838 RCV000022839 RCV000022840 RCV000477909 RCV000033153 RCV001253092	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Myopathy, distal, 7, adult-onset, X-linked	Pathogenic	rs2147387003, rs2147390527, rs2147396459, rs770287561	RCV002221692 RCV002221982 RCV002221983 RCV002221984	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
X-linked deafness	Pathogenic	rs1569308571	RCV000626484	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
DEAFNESS, X-LINKED 1	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEAFNESS, X-LINKED 4	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SMPX-related disorder	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED ISOLATED SENSORINEURAL HEARING LOSS TYPE DFN	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
X-LINKED NONSYNDROMIC HEARING LOSS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Angioedemas, Hereditary	Angioedema	BEFREE	28251901, 29998524		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	21520243, 27066863		★☆☆☆☆ Found in Text Mining only
Deafness	Deafness	Pubtator	28542515, 31478598, 31992338, 34052664	Associate	★☆☆☆☆ Found in Text Mining only
DEAFNESS, X-LINKED 4 (disorder)	Deafness	CLINVAR_DG	21549336, 21549342		★☆☆☆☆ Found in Text Mining only
DEAFNESS, X-LINKED 4 (disorder)	Deafness	BEFREE	21893181		★☆☆☆☆ Found in Text Mining only
DEAFNESS, X-LINKED 4 (disorder)	Deafness	GENOMICS_ENGLAND_DG	8872482		★☆☆☆☆ Found in Text Mining only
DEAFNESS, X-LINKED 4 (disorder)	Deafness	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Dermatitis	Dermatitis	BEFREE	28472118		★☆☆☆☆ Found in Text Mining only
Distal Myopathies	Distal myopathy	Pubtator	33974137	Associate	★☆☆☆☆ Found in Text Mining only
Glioblastoma	Glioblastoma	BEFREE	23451269		★☆☆☆☆ Found in Text Mining only
Glioblastoma Multiforme	Glioblastoma	BEFREE	23451269		★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	28542515, 31478598, 34052664, 39272213	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss, High-Frequency	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hodgkin Disease	Hodgkin Disease	BEFREE	28542515		★☆☆☆☆ Found in Text Mining only
Kaposi Sarcoma	Kaposi Sarcoma	BEFREE	31308175		★☆☆☆☆ Found in Text Mining only
leukemia	Leukemia	BEFREE	19349467		★☆☆☆☆ Found in Text Mining only
Li-Fraumeni-Like Syndrome	Li-Fraumeni Syndrome	BEFREE	28608266		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	21520243, 27066863		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of skin	Skin cancer	BEFREE	30231994		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21520243, 26302407, 27542230, 28684431, 31467287		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	18339869		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	22682244, 27066863, 29757189, 30231994		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	30770291		★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	CLINGEN_DG	21519551, 21549336, 21549342, 21893181, 22911656, 28542515		★☆☆☆☆ Found in Text Mining only
Nonsyndromic Deafness	Nonsyndromic Deafness	BEFREE	28542515, 30874365		★☆☆☆☆ Found in Text Mining only
Progressive hearing loss stapes fixation	Hearing loss with stapes fixation	Pubtator	31478598	Associate	★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	BEFREE	29559740		★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma	Carcinoma	BEFREE	26302407, 27542230, 29757189		★☆☆☆☆ Found in Text Mining only
Squamous cell carcinoma of skin	Skin carcinoma	BEFREE	31467287		★☆☆☆☆ Found in Text Mining only
von Willebrand Disease	von Willebrand disorder	BEFREE	27203734		★☆☆☆☆ Found in Text Mining only
X-linked non-syndromic sensorineural deafness type DFN	Deafness, X-Linked	Orphanet			★☆☆☆☆ Found in Text Mining only