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.

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.

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				14	11	25
missense			48	1	3	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	48	15	14

Variants in TGM2

This is a list of pathogenic ClinVar variants found in the TGM2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-38130225-G-A			Likely benign (Mar 28, 2018)
20-38130278-C-T		not specified	Uncertain significance (Aug 04, 2024)
20-38130290-C-A		not specified	Uncertain significance (Dec 06, 2024)
20-38130315-C-T			Likely benign (Mar 29, 2018)
20-38130356-C-T		not specified	Uncertain significance (Sep 25, 2023)
20-38130360-G-A			Benign (Dec 31, 2019)
20-38130364-T-C		not specified	Uncertain significance (Feb 22, 2023)
20-38130368-G-A		not specified	Uncertain significance (Sep 26, 2023)
20-38131096-T-A		not specified	Uncertain significance (Oct 09, 2024)
20-38131100-C-G		not specified	Uncertain significance (Apr 25, 2023)
20-38131101-C-T			Benign (Jun 14, 2018)
20-38131115-C-G		not specified	Uncertain significance (Mar 01, 2025)
20-38131129-C-G		not specified	Uncertain significance (Jun 16, 2023)
20-38131150-C-T		not specified	Uncertain significance (Mar 05, 2025)
20-38131210-T-A		not specified	Uncertain significance (Dec 11, 2023)
20-38131216-G-A		not specified	Uncertain significance (Oct 25, 2024)
20-38132341-C-T		not specified	Uncertain significance (Aug 13, 2021)
20-38132350-A-G		not specified	Uncertain significance (Feb 12, 2024)
20-38132384-C-T		not specified	Uncertain significance (May 08, 2023)
20-38132407-G-A		not specified	Uncertain significance (May 30, 2023)
20-38132480-T-C		not specified	Uncertain significance (Sep 27, 2021)
20-38132492-C-A			Benign (Dec 31, 2019)
20-38138189-G-A			Likely benign (Jun 08, 2018)
20-38138211-C-T		not specified	Uncertain significance (Dec 20, 2023)
20-38138230-C-T		not specified	Uncertain significance (Jan 22, 2024)

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