TGM3

protein-coding

transglutaminase 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

NM_003245.4

Inheritance

AR

ClinVar variants

P:1U:131B:29

Top phenotype

Uncombable hair syndrome 2

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr20:2,296,001-2,341,079

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~45.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

uncombable hair syndrome 2MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014989

Submitter: PanelApp Australia

uncombable hair syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0008621

Submitter: Orphanet

uncombable hair syndrome 2LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014989

Submitter: G2P

Clinical Genomic Database (CGD)

Uncombable hair syndrome 2AR

Manifestation: Dermatologic

Intervention: General

Rationale: The clinical relevance of the condition is unclear

Refs: 27866708Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TGM3 variants in ClinVar

4 Conditions Cataloged
not specifiedTotal: 128
TGM3-related disorderTotal: 21
not providedTotal: 11
Uncombable hair syndrome 2Total: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
12
clinvar
5
clinvar
18
missense
127
clinvar
8
clinvar
4
clinvar
139
nonsense
1
clinvar
1
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
3
clinvar
3
Total10131209161

Highest pathogenic variant AF is 0.000034338773

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003245.4RefSeqNP_003236.313MANE Select
ENST00000381458.6EnsemblENSP00000370867.513MANE Select
ENST00001132636.1EnsemblENSP00000811238.113Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.4114474231.060.00002674568
Missense (PolyPhen)159163.060.975121815
Synonymous-1.181981781.110.00001271363
Loss of Function2.981533.70.4460.00000178342

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.000170.00017rare
Ashkenazi Jewish00.0absent
East Asian0.000160.00016rare
Finnish00.0absent
European (Non-Finnish)0.000290.00029rare
South Asian0.000230.00023rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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