TGM2

transglutaminase 2, the group of Transglutaminases

Basic information

Region (hg38): 20:38127385-38166578

Links

ENSG00000198959

∙ NCBI:7052 ∙ OMIM:190196 ∙ HGNC:11778 ∙ Uniprot:P21980 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

type 2 diabetes mellitus (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TGM2 gene.

not_specified (83 variants)
not_provided (31 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TGM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004613.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				14 clinvar	12 clinvar	26
missense			83 clinvar	1 clinvar	3 clinvar	87
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	83	15	15

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TGM2	protein_coding	protein_coding	ENST00000361475	13	38118

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.81e-18	0.0271	125626	0	122	125748	0.000485

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.536	400	431	0.927	0.0000299	4487
Missense in Polyphen		127	156.77	0.81011		1594
Synonymous	-0.467	196	188	1.04	0.0000141	1336
Loss of Function	0.703	29	33.4	0.869	0.00000172	356

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000761	0.000757
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000554	0.000554
European (Non-Finnish)	0.000330	0.000325
Middle Eastern	0.0000544	0.0000544
South Asian	0.00158	0.00154
Other	0.000835	0.000815

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the cross-linking of proteins and the conjugation of polyamines to proteins.;
Pathway: Huntington,s disease - Homo sapiens (human);phospholipase c delta in phospholipid associated cell signaling;Thromboxane A2 receptor signaling;Alpha9 beta1 integrin signaling events;Beta1 integrin cell surface interactions (Consensus)

Recessive Scores

pRec: 0.707

Intolerance Scores

loftool: 0.248
rvis_EVS: -0.84
rvis_percentile_EVS: 11.48

Haploinsufficiency Scores

pHI: 0.275
hipred: N
hipred_score: 0.407
ghis: 0.521

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.962

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tgm2
Phenotype: immune system 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); hematopoietic system phenotype; 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); 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); neoplasm; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process: blood vessel remodeling;isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine;negative regulation of endoplasmic reticulum calcium ion concentration;positive regulation of apoptotic process;positive regulation of I-kappaB kinase/NF-kappaB signaling;apoptotic cell clearance;positive regulation of cell adhesion;positive regulation of smooth muscle cell proliferation;positive regulation of inflammatory response;protein homooligomerization;positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway;positive regulation of mitochondrial calcium ion concentration;branching involved in salivary gland morphogenesis;salivary gland cavitation
Cellular component: mitochondrion;endoplasmic reticulum;cytosol;focal adhesion;intrinsic component of plasma membrane;collagen-containing extracellular matrix;extracellular exosome
Molecular function: protein-glutamine gamma-glutamyltransferase activity;protein binding;GTP binding;protein domain specific binding;metal ion binding