MESP2 (mesoderm posterior bHLH transcription factor 2)

Gene

• Entrez ID: 145873
• Gene name: Mesoderm posterior bHLH transcription factor 2
• Gene symbol: MESP2
• Synonyms (NCBI Gene): SCDO2, bHLHc6
• Chromosome: 15
• Chromosome location: 15q26.1
• Summary: This gene encodes a member of the bHLH family of transcription factors and plays a key role in defining the rostrocaudal patterning of somites via interactions with multiple Notch signaling pathways. This gene is expressed in the anterior presomitic mesod

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs71647806	C>G	Pathogenic	Missense variant, coding sequence variant
rs71647808	G>A,C,T	Pathogenic	Missense variant, stop gained, coding sequence variant
rs113994156	A>G	Pathogenic	Missense variant, coding sequence variant
rs113994157	A>G,T	Pathogenic	Missense variant, coding sequence variant
rs113994158	->ACCG	Pathogenic	Coding sequence variant, frameshift variant
rs118204034	G>A,C,T	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs118204035	G>T	Pathogenic	Coding sequence variant, stop gained
rs538996447	G>A,T	Likely-pathogenic	Stop gained, coding sequence variant, missense variant
rs762067626	C>A,T	Likely-pathogenic	Missense variant, stop gained, coding sequence variant
rs912110093	G>A,C	Likely-pathogenic	Stop gained, coding sequence variant, missense variant
rs1206731716	C>A,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant
rs1452984345	CAGC>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555439013	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1555439049	->GCAGAGCG	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555439061	->GC	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1555439063	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1555439118	C>T	Likely-pathogenic	Stop gained, coding sequence variant
rs1555439152	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1596154534	->G	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT021550	hsa-miR-142-3p	Microarray	17612493
MIRT1143303	hsa-miR-22	CLIP-seq
MIRT1143304	hsa-miR-2909	CLIP-seq
MIRT2270475	hsa-miR-1193	CLIP-seq
MIRT2270476	hsa-miR-1343	CLIP-seq
MIRT2270477	hsa-miR-3169	CLIP-seq
MIRT2270478	hsa-miR-3688-3p	CLIP-seq
MIRT2270479	hsa-miR-3690	CLIP-seq
MIRT2270480	hsa-miR-3978	CLIP-seq
MIRT2270481	hsa-miR-4254	CLIP-seq
MIRT2270482	hsa-miR-4740-5p	CLIP-seq
MIRT2270483	hsa-miR-583	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000978	Function	RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001707	Process	Mesoderm formation	IBA
GO:0003007	Process	Heart morphogenesis	IBA
GO:0003677	Function	DNA binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007219	Process	Notch signaling pathway	IEA
GO:0032525	Process	Somite rostral/caudal axis specification	IBA
GO:0046983	Function	Protein dimerization activity	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

Other IDs

• MIM: 605195
• HGNC: 29659
• e!Ensembl: ENSG00000188095

Protein

• UniProt ID: Q0VG99
• Protein name: Mesoderm posterior protein 2 (Class C basic helix-loop-helix protein 6) (bHLHc6)
• Protein function: Transcription factor with important role in somitogenesis. Defines the rostrocaudal patterning of the somite by participating in distinct Notch pathways. Also regulates the FGF signaling pathway. Specifies the rostral half of the somites. Genera
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00010	HLH	82 → 136	Helix-loop-helix DNA-binding domain	Domain

• Sequence:

  MAQSPPPQSLLGHDHWIFAQGWGWAGHWDSTSPASSSDSSGSCPCDGARGLPQPQPPSCS
  SRAAEAAATTPRRARTGPAGGQRQSASEREKLRMRTLARALHELRRFLPPSLAPAGQSLT
  KIETLRLAIRYIGHLSAVLGLSEESLQCRRRQRGDAGSPWGCPLCPDRGPAEAQTQAEGQ
  GQGQGQGQGQGQGQGQGQGQGQGQGRRPGLVSAVLAEASWGSPSACPGAQAAPERLGRGV
  HDTDPWATPPYCPKIQSPPYSSQGTTSDASLWTPPQGCPWTQSSPEPRNPPVPWTAAPAT
  LELAAVYQGLSVSPEPCLSLGAPSLLPHPSCQRLQPQTPGRCWSHSAEVVPNSEDQGPGA
  AFQLSEASPPQSSGLRFSGCPELWQEDLEGARLGIFY

• Sequence length: 397

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
Spondylocostal dysostosis 2, autosomal recessive	Pathogenic; Likely pathogenic	rs113994158, rs71647808, rs118204035, rs2505184685, rs2505184605, rs118204034, rs1555439013, rs1555439118, rs912110093, rs762067626, rs1452984345, rs1555439061, rs538996447, rs1555439152, rs1206731716, rs1555439049, rs1555439063	RCV000005492 RCV000005493 RCV000005495 RCV003236476 RCV003388863 RCV000032155 RCV000670586 RCV000673076 RCV000667887 RCV000673463 RCV000671183 RCV000673120 RCV000666082 RCV000669986 RCV000671724 RCV000673749 RCV000666771	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
AUTOSOMAL RECESSIVE SPONDYLOCOSTAL DYSOSTOSIS	—	Disgenet, Orphanet Disgenet, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ANEURYSM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DESBUQUOIS SYNDROME	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GASTROPARESIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JARCHO-LEVIN SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
JUVENILE IDIOPATHIC ARTHRITIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MESP2-related disorder	Likely benign; Benign; Conflicting classifications of pathogenicity; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spondylocostal dysostosis	Likely benign; Benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPONDYLOCOSTAL DYSOSTOSIS 1, AUTOSOMAL RECESSIVE	—	ClinVar, HPO ClinVar, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPONDYLOCOSTAL DYSOSTOSIS 3, AUTOSOMAL RECESSIVE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPONDYLOCOSTAL DYSOSTOSIS, AUTOSOMAL RECESSIVE	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acquired Kyphoscoliosis	Acquired Kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anemia, Sickle Cell	Anemia	BEFREE	21038776		★☆☆☆☆ Found in Text Mining only
Autosomal recessive spondylocostal dysostosis	Spondylocostal Dysostosis	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital diaphragmatic hernia	Congenital diaphragmatic hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital exomphalos	Congenital Exomphalos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital fusion of ribs	Rib fusion	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital kyphoscoliosis	Congenital kyphoscoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital meningocele	Congenital Meningocele	HPO_DG			★☆☆☆☆ Found in Text Mining only
Coronary Aneurysm	Coronary Aneurysm	GWASCAT_DG	27171184		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Defect of vertebral segmentation	Abnormal spinal segmentation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysostoses	Dysostoses	LHGDN	15122512, 18485326		★☆☆☆☆ Found in Text Mining only
Dysostoses	Dysphoric mood	Pubtator	16385447	Associate	★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Jarcho-Levin syndrome	Jarcho-Levin Syndrome	BEFREE	15122512, 18485326, 21038776		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Jarcho-Levin syndrome	Jarcho-Levin Syndrome	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Jarcho-Levin syndrome	Jarcho-Levin Syndrome	GENOMICS_ENGLAND_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mucocutaneous Lymph Node Syndrome	Kawasaki disease	GWASCAT_DG	27171184		★☆☆☆☆ Found in Text Mining only
Pulmonary Venous Return Anomaly	Pulmonary Venous Return Anomaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Renal carnitine transport defect	Renal Carnitine Transport Defect	BEFREE	21038776		★☆☆☆☆ Found in Text Mining only
Scoliosis, unspecified	Scoliosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spina Bifida Occulta	Spina bifida occulta	HPO_DG			★☆☆☆☆ Found in Text Mining only
SPONDYLOCOSTAL DYSOSTOSIS 5	Spondylocostal Dysostosis	BEFREE	18485326		★☆☆☆☆ Found in Text Mining only
SPONDYLOCOSTAL DYSOSTOSIS, AUTOSOMAL RECESSIVE 2	Spondylocostal Dysostosis	GENOMICS_ENGLAND_DG	15122512, 18485326		★☆☆☆☆ Found in Text Mining only
SPONDYLOCOSTAL DYSOSTOSIS, AUTOSOMAL RECESSIVE 2	Spondylocostal Dysostosis	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
SPONDYLOCOSTAL DYSOSTOSIS, AUTOSOMAL RECESSIVE 2	Spondylocostal Dysostosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
SPONDYLOCOSTAL DYSOSTOSIS, AUTOSOMAL RECESSIVE 3	Spondylocostal Dysostosis	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
Syndactyly of fingers	Syndactyly of fingers	HPO_DG			★☆☆☆☆ Found in Text Mining only