MEST

mesoderm specific transcript, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 7:130486170-130506465

Links

ENSG00000106484 ∙ NCBI:4232 ∙ OMIM:601029 ∙ HGNC:7028 ∙ Uniprot:Q5EB52 ∙ 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 MEST gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEST 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						0
missense		1	13	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	13	1	0

Variants in MEST

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

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

Position	Type	Phenotype	Significance	ClinVar
7-130495369-A-G		not specified	Uncertain significance (Mar 18, 2024)
7-130495373-G-A		not specified	Uncertain significance (Jan 22, 2024)
7-130495423-T-C		not specified	Uncertain significance (Oct 03, 2023)
7-130495507-C-G		not specified	Uncertain significance (Aug 30, 2021)
7-130497955-T-G		not specified	Uncertain significance (Feb 05, 2024)
7-130498193-C-T		not specified	Uncertain significance (Feb 27, 2023)
7-130498211-A-T		not specified	Uncertain significance (Feb 03, 2022)
7-130498251-T-C		not specified	Likely benign (May 27, 2022)
7-130498265-C-A		not specified	Uncertain significance (Sep 06, 2022)
7-130499896-G-A		not specified	Uncertain significance (Jul 13, 2021)
7-130499898-C-T		Childhood-onset schizophrenia	Likely pathogenic (Jan 01, 2014)
7-130500799-G-A		not specified	Uncertain significance (Sep 27, 2021)
7-130500804-T-G		not specified	Uncertain significance (Jul 05, 2022)
7-130502661-A-G		not specified	Uncertain significance (Mar 17, 2023)
7-130503980-T-C		not specified	Uncertain significance (Jan 26, 2022)
7-130504956-C-G		not specified	Uncertain significance (Aug 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEST	protein_coding	protein_coding	ENST00000223215	12	20122

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.399	0.601	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	101	193	0.523	0.0000110	2166
Missense in Polyphen		16	59.57	0.26859		792
Synonymous	0.592	66	72.4	0.911	0.00000409	663
Loss of Function	3.42	5	22.5	0.222	0.00000121	242

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.223

Intolerance Scores

• loftool: 0.154
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.510
• hipred: Y
• hipred_score: 0.765
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mest
• Phenotype: growth/size/body region phenotype; cellular phenotype; muscle 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); embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: mesoderm development;regulation of lipid storage
• Cellular component: endoplasmic reticulum;endoplasmic reticulum membrane;integral component of membrane;extracellular exosome
• Molecular function: hydrolase activity