MESP1

mesoderm posterior bHLH transcription factor 1, the group of Basic helix-loop-helix proteins

Basic information

Region (hg38): 15:89749874-89751249

Links

ENSG00000166823 ∙ NCBI:55897 ∙ OMIM:608689 ∙ HGNC:29658 ∙ Uniprot:Q9BRJ9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MESP1 gene.

• not provided (50 variants)
• Inborn genetic diseases (19 variants)
• Congenital heart disease (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MESP1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				6	8	14
missense			33	1	12	46
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel			1		1	2
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	36	7	21

Variants in MESP1

This is a list of pathogenic ClinVar variants found in the MESP1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-89750192-G-C		MESP1-related disorder	Benign/Likely benign (Aug 05, 2022)
15-89750205-G-A		MESP1-related disorder	Uncertain significance (Oct 20, 2023)
15-89750208-A-G			Uncertain significance (May 25, 2023)
15-89750225-G-C			Likely benign (Jul 16, 2023)
15-89750235-G-A			Likely benign (Mar 08, 2022)
15-89750497-G-A			Likely benign (Aug 30, 2023)
15-89750545-A-C		MESP1-related disorder	Benign (Feb 01, 2024)
15-89750563-G-C		MESP1-related disorder	Benign (Feb 01, 2024)
15-89750571-C-A			Uncertain significance (Sep 22, 2022)
15-89750575-C-A		MESP1-related disorder	Benign (Jan 30, 2024)
15-89750582-C-T		MESP1-related disorder	Benign (Jan 13, 2024)
15-89750605-T-C			Likely benign (Dec 12, 2023)
15-89750607-C-G		not specified	Uncertain significance (Jun 13, 2023)
15-89750608-G-A			Likely benign (Mar 26, 2022)
15-89750664-C-A		not specified	Uncertain significance (Jan 18, 2022)
15-89750671-G-A			Likely benign (Feb 16, 2023)
15-89750672-C-A		not specified	Uncertain significance (Nov 06, 2023)
15-89750672-CGCCCCT-C			Uncertain significance (Feb 11, 2023)
15-89750706-T-A			Likely benign (Sep 10, 2021)
15-89750712-T-C		MESP1-related disorder	Benign (Dec 02, 2023)
15-89750729-T-C		MESP1-related disorder	Benign (Aug 04, 2023)
15-89750733-G-C		not specified	Uncertain significance (Jan 16, 2024)
15-89750733-G-T		not specified	Uncertain significance (Dec 18, 2023)
15-89750763-C-A			Uncertain significance (Dec 21, 2023)
15-89750767-A-C		MESP1-related disorder	Likely benign (Jun 05, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MESP1	protein_coding	protein_coding	ENST00000300057	2	2650

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000861	0.193	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.348	74	82.9	0.892	0.00000391	1552
Missense in Polyphen		25	30.275	0.82576		500
Synonymous	0.0186	39	39.1	0.996	0.00000192	591
Loss of Function	-1.09	5	2.97	1.68	1.28e-7	55

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcription factor. Plays a role in the epithelialization of somitic mesoderm and in the development of cardiac mesoderm. Defines the rostrocaudal patterning of the somites by participating in distinct Notch pathways (By similarity). {ECO:0000250}.
• Pathway: Cardiac Progenitor Differentiation (Consensus)

Recessive Scores

• pRec: 0.123

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.139

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.127

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Mesp1
• Phenotype: endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; respiratory system phenotype; embryo phenotype; skeleton phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: mespbb
• Affected structure: determination of heart left/right asymmetry
• Phenotype tag: abnormal
• Phenotype quality: decreased efficacy

Gene ontology

• Biological process: mesoderm formation;somitogenesis;heart looping;heart morphogenesis;secondary heart field specification;embryonic heart tube morphogenesis;cardiac atrium formation;cardiac ventricle formation;sinus venosus morphogenesis;growth involved in heart morphogenesis;cardioblast anterior-lateral migration;Notch signaling pathway;gastrulation;mesodermal cell migration;neurogenesis;signal transduction involved in regulation of gene expression;positive regulation of Notch signaling pathway involved in heart induction;negative regulation of mesodermal cell fate specification;negative regulation of endodermal cell fate specification;endothelial cell differentiation;positive regulation of Notch signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;lateral mesoderm development;positive regulation of striated muscle cell differentiation;cardiac muscle cell differentiation;cardiac cell fate determination;sinoatrial node cell differentiation;cardiac vascular smooth muscle cell differentiation;cardioblast migration to the midline involved in heart field formation;positive regulation of hepatocyte differentiation;positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;enhancer binding;transcription regulatory region DNA binding;protein dimerization activity