TGM3
protein-codingtransglutaminase 3, the group of Transglutaminases
Gene summary
Transglutaminases are enzymes that catalyze the crosslinking of proteins by epsilon-gamma glutamyl lysine isopeptide bonds. While the primary structure of transglutaminases is not conserved, they all have the same amino acid sequence at their active sites and their activity is calcium-dependent. The protein encoded by this gene consists of two polypeptide chains activated from a single precursor protein by proteolysis. The encoded protein is involved the later stages of cell envelope formation in the epidermis and hair follicle. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~45.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014989
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0008621
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014989
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Dermatologic
Intervention: General
Rationale: The clinical relevance of the condition is unclear
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TGM3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003245.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 12 | 5 | 18 | ||
| missense | 127 | 8 | 4 | 139 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 1 | 0 | 131 | 20 | 9 | 161 |
Highest pathogenic variant AF is 0.000034338773
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003236.3 | 13 | MANE Select | |
| Ensembl | ENSP00000370867.5 | 13 | MANE Select | |
| Ensembl | ENSP00000811238.1 | 13 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cellular protein modification process
- peptide cross-linking
- keratinocyte differentiation
- hair follicle morphogenesis
- keratinization
Molecular Function
- protein-glutamine gamma-glutamyltransferase activity
- catalytic activity
- calcium ion binding
- transferase activity, transferring acyl groups
Cellular Component
- cytoplasm
- extrinsic component of cytoplasmic side of plasma membrane
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000381458
- Coding exons
- 13
- Length
- 45078
- Individuals with no LoFs
- 125695
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 52
- Defined
- 125747
- p
- 0.000207
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.411 | 447 | 423 | 1.06 | 0.0000267 | 4568 |
| Missense (PolyPhen) | 159 | 163.06 | 0.97512 | 1815 | ||
| Synonymous | -1.18 | 198 | 178 | 1.11 | 0.0000127 | 1363 |
| Loss of Function | 2.98 | 15 | 33.7 | 0.446 | 0.00000178 | 342 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00017 | 0.00017 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00029 | 0.00029 | rare |
| South Asian | 0.00023 | 0.00023 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the calcium-dependent formation of isopeptide cross-links between glutamine and lysine residues in various proteins, as well as the conjugation of polyamines to proteins. Involved in the formation of the cornified envelope (CE), a specialized component consisting of covalent cross-links of proteins beneath the plasma membrane of terminally differentiated keratinocytes. Catalyzes small proline-rich proteins (SPRR1 and SPRR2) and LOR cross-linking to form small interchain oligomers, which are further cross-linked by TGM1 onto the growing CE scaffold (By similarity). In hair follicles, involved in cross- linking structural proteins to hardening the inner root sheath. {ECO:0000250}.;
- Disease
- DISEASE: Uncombable hair syndrome 2 (UHS2) [MIM:617251]: A form of uncombable hair syndrome, a condition characterized by scalp hair that is impossible to comb due to the haphazard arrangement of the hair bundles. A characteristic morphologic feature is a triangular to reniform to heart shape on cross-sections, and a groove, canal or flattening along the entire length of the hair. Most individuals are affected early in childhood and the hair takes on a spun-glass appearance with the hair becoming dry, curly, glossy, lighter in color, and progressively uncombable. The hair growth rate can range from slow to normal, and the condition improves with age. {ECO:0000269|PubMed:27866708}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.219
Intolerance Scores
- LoFtool
- 0.320
- RVIS EVS
- -0.21
- RVIS percentile EVS
- 37.76
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.538
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |