Dyskeratosis congenita, autosomal dominant 3

disease
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Also known as DKCA3dyskeratosis congenita, autosomal dominant type 3

Summary

Dyskeratosis congenita, autosomal dominant 3 (MONDO:0013522) is a disease caused by TINF2 (GenCC Definitive), with 3 cohort genes.

At a glance

  • Causal gene: TINF2 (GenCC Definitive)
  • Cohort genes: 3
  • ClinVar variants: 83

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namedyskeratosis congenita, autosomal dominant 3
Mondo IDMONDO:0013522
OMIM613990
DOIDDOID:0070018
NCITC176923
UMLSC3151445
MedGen462795
GARD0015742
Is cancer (heuristic)no

Also known as: DKCA3 · dyskeratosis congenita, autosomal dominant 3 · dyskeratosis congenita, autosomal dominant type 3

Data availability: 83 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › autosomal genetic disease › autosomal dominant disease › dyskeratosis congenita, autosomal dominant 3

Related subtypes (191): autosomal dominant polycystic liver disease, cerebral arteriopathy, autosomal dominant, with subcortical infarcts and leukoencephalopathy, type 1, tuberous sclerosis, Treacher-Collins syndrome, hereditary breast ovarian cancer syndrome, autosomal dominant polycystic kidney disease, Lynch syndrome, branchio-oto-renal syndrome, autosomal dominant Aarskog syndrome, acroosteolysis dominant type, ADULT syndrome, autosomal dominant Alport syndrome, amelogenesis imperfecta type 1B, Townes-Brocks syndrome, nevoid basal cell carcinoma syndrome, blepharophimosis, ptosis, and epicanthus inversus syndrome, autosomal dominant brachyolmia, branchiooculofacial syndrome, pheochromocytoma/paraganglioma syndrome 4, cataract-aberrant oral frenula-growth delay syndrome, cherubism, autosomal dominant chondrodysplasia punctata, autosomal dominant popliteal pterygium syndrome, blepharocheilodontic syndrome, cochleosaccular degeneration-cataract syndrome, renal coloboma syndrome, Beare-Stevenson cutis gyrata syndrome, autosomal dominant vibratory urticaria, neurohypophyseal diabetes insipidus, autosomal dominant Kenny-Caffey syndrome, Rapp-Hodgkin syndrome, Ehlers-Danlos syndrome, classic type, autosomal dominant Ehlers-Danlos syndrome, vascular type, multiple endocrine neoplasia type 1, Coffin-Siris syndrome 1, isolated congenital adermatoglyphia, Flynn-Aird syndrome, Frasier syndrome, hand-foot-genital syndrome, Holt-Oram syndrome, hyperkeratosis-hyperpigmentation syndrome, autosomal dominant ichthyosis vulgaris, hyper-IgE recurrent infection syndrome 1, autosomal dominant, autosomal dominant keratitis, autosomal dominant keratitis-ichthyosis-hearing loss syndrome, LADD syndrome, trichorhinophalangeal syndrome type II, Noonan syndrome with multiple lentigines, microcephaly with or without chorioretinopathy, lymphedema, or intellectual disability, Marfan syndrome, melanoma, cutaneous malignant, susceptibility to, 2, autosomal dominant primary microcephaly, autosomal dominant progressive external ophthalmoplegia, monilethrix, Muir-Torre syndrome, autosomal dominant myoglobinuria, autosomal dominant centronuclear myopathy, nail-patella syndrome, multiple endocrine neoplasia type 2B, autosomal dominant omodysplasia, pheochromocytoma/paraganglioma syndrome 1, Pelger-Huet anomaly, multiple endocrine neoplasia type 2A, piebaldism, autosomal dominant medullary cystic kidney disease with or without hyperuricemia, generalized juvenile polyposis/juvenile polyposis coli, juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome, Peutz-Jeghers syndrome, contractures, pterygia, and spondylocarpotarsal fusion syndrome 1A, autosomal dominant distal renal tubular acidosis, retinoschisis, autosomal dominant, autosomal dominant Robinow syndrome, scapuloperoneal spinal muscular atrophy, autosomal dominant, autosomal dominant sideroblastic anemia, spondyloepiphyseal dysplasia tarda, autosomal dominant, proximal symphalangism, calcaneonavicular coalition, thanatophoric dysplasia type 1, trichorhinophalangeal syndrome type I, Muckle-Wells syndrome, autosomal dominant hypophosphatemic rickets, von Hippel-Lindau disease, Denys-Drash syndrome, autosomal dominant severe congenital neutropenia, Costello syndrome, EEC syndrome, multiple cutaneous and mucosal venous malformations, diffuse nonepidermolytic palmoplantar keratoderma, Timothy syndrome, pheochromocytoma/paraganglioma syndrome 2, spondyloepimetaphyseal dysplasia with multiple dislocations, Brooke-Spiegler syndrome, macrocephaly-autism syndrome, pheochromocytoma/paraganglioma syndrome 3, Duane-radial ray syndrome, PCWH syndrome, heart-hand syndrome, Slovenian type, congenital stationary night blindness autosomal dominant 3, mandibulofacial dysostosis-microcephaly syndrome, multiple endocrine neoplasia type 4, juvenile cataract-microcornea-renal glucosuria syndrome, Crouzon syndrome-acanthosis nigricans syndrome, Birk-Barel syndrome, thrombophilia due to protein S deficiency, autosomal dominant, dyskeratosis congenita, autosomal dominant 2, colorectal cancer, hereditary nonpolyposis, type 6, colorectal cancer, hereditary nonpolyposis, type 7, brain small vessel disease 2A, autosomal dominant, intellectual disability, autosomal dominant 14, intellectual disability, autosomal dominant 15, intellectual disability, autosomal dominant 16, hypopigmentation-punctate palmoplantar keratoderma syndrome, intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency, postaxial polydactyly-anterior pituitary anomalies-facial dysmorphism syndrome, intellectual developmental disorder with microcephaly and with or without ocular malformations or hypogonadotropic hypogonadism, intellectual disability, autosomal dominant 29, intellectual disability, autosomal dominant 30, Houge-Janssens syndrome 2, severe achondroplasia-developmental delay-acanthosis nigricans syndrome, dyskeratosis congenita, autosomal dominant 6, epidermolysis bullosa simplex 6, generalized, with scarring and hair loss, autosomal dominant complex spastic paraplegia, early-onset autosomal dominant Alzheimer disease, muscular dystrophy, limb-girdle, autosomal dominant, Feingold syndrome, Carney complex, neuronopathy, distal hereditary motor, autosomal dominant, autosomal dominant coarctation of aorta, autosomal dominant spondylocostal dysostosis, autosomal dominant hypohidrotic ectodermal dysplasia, Cowden disease, autosomal dominant distal myopathy, autosomal dominant rhegmatogenous retinal detachment, palmoplantar keratoderma-spastic paralysis syndrome, Alagille syndrome due to a JAG1 point mutation, PTEN hamartoma tumor syndrome, gastric adenocarcinoma and proximal polyposis of the stomach, autosomal dominant proximal renal tubular acidosis, autosomal dominant spastic ataxia, Waardenburg syndrome, hereditary retinoblastoma, autosomal dominant hypocalcemia, Li-Fraumeni syndrome, Loeys-Dietz syndrome, hereditary hemorrhagic telangiectasia, hereditary inclusion body myopathy-joint contractures-ophthalmoplegia syndrome, microcephalic osteodysplastic dysplasia, Saul-Wilson type, autosomal dominant intermediate Charcot-Marie-Tooth disease, autosomal dominant cutis laxa, autosomal dominant nonsyndromic hearing loss, autosomal dominant optic atrophy, autosomal dominant Emery-Dreifuss muscular dystrophy, autosomal dominant cerebellar ataxia, autosomal dominant osteopetrosis, autosomal dominant epidermolytic ichthyosis, ventricular arrhythmias due to cardiac ryanodine receptor calcium release deficiency syndrome, distal arthrogryposis type 2B1, neurofibromatosis, autosomal dominant cataract, arthrogryposis, distal, type 2B2, arthrogryposis, distal, type 2B3, Charcot-Marie-Tooth disease, demyelinating, type 1G, Delpire-McNeill syndrome, LAMA5-related multisystemic syndrome, autosomal dominant oculocutaneous albinism, Charcot-Marie-tooth disease, axonal, type 2DD, Pilarowski-Bjornsson syndrome, intellectual disability, autosomal dominant, fatty acyl-CoA reductase 1 upregulation, GUCY2D-related dominant retinopathy, RPE65-related dominant retinopathy, autosomal dominant titinopathy, NOG-related symphalangism spectrum disorder, ALPL-related autosomal dominant hypophosphatasia, MYH10-related neurodevelopmental disorder with congenital anomalies, spastic paraplegia 30A, autosomal dominant, TMEM127-related tumor predisposition, MAX-related tumor predisposition, BMPR1A-related juvenile polyposis syndrome, RP1-related dominant retinopathy, Birt-Hogg-Dube syndrome, inclusion body myopathy and brain white matter abnormalities, KINSSHIP syndrome, autosomal dominant nebulin-related myopathy, IMPG1-related dominant retinopathy, PROM1-related dominant retinopathy, PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome, ALG8-related autosomal dominant polycystic kidney and/or liver disease, NOTCH1-related AOS spectrum disorder, FLNB-associated autosomal dominant filamin related bone disorder, familial antiphospholipid syndrome

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

83 retrieved; paginated sample, class counts are floors:

43 uncertain significance, 12 conflicting classifications of pathogenicity, 11 benign/likely benign, 8 pathogenic, 5 benign, 2 likely benign, 2 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
31541NM_001099274.3(TINF2):c.805C>T (p.Gln269Ter)TINF2Pathogenicno assertion criteria provided
31543NM_001099274.3(TINF2):c.811C>T (p.Gln271Ter)TINF2Pathogenicno assertion criteria provided
37090NM_001099274.3(TINF2):c.826del (p.Arg276fs)TINF2Pathogenicno assertion criteria provided
4056134NM_001099274.3(TINF2):c.848_849dup (p.Thr284fs)TINF2Pathogeniccriteria provided, single submitter
5624NM_001099274.3(TINF2):c.838A>G (p.Lys280Glu)TINF2Pathogeniccriteria provided, single submitter
5625NM_001099274.3(TINF2):c.845G>A (p.Arg282His)TINF2Pathogeniccriteria provided, multiple submitters, no conflicts
5626NM_001099274.3(TINF2):c.844C>A (p.Arg282Ser)TINF2Pathogeniccriteria provided, single submitter
5627NM_001099274.3(TINF2):c.844C>T (p.Arg282Cys)TINF2Pathogeniccriteria provided, multiple submitters, no conflicts
3237357NM_001099274.3(TINF2):c.865C>G (p.Pro289Ala)TINF2Likely pathogeniccriteria provided, single submitter
3576544NM_001099274.3(TINF2):c.848C>T (p.Pro283Leu)TINF2Likely pathogeniccriteria provided, single submitter
312957NM_001099274.3(TINF2):c.62A>G (p.Gln21Arg)LOC130055403Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
417880NM_001099274.3(TINF2):c.81C>A (p.Cys27Ter)LOC130055403Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
312958NM_001099274.3(TINF2):c.-50A>GLOC130055404Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
38918NM_001099274.3(TINF2):c.841G>A (p.Glu281Lys)TGM1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
280299NM_001099274.3(TINF2):c.936C>A (p.Tyr312Ter)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
312948NM_001099274.3(TINF2):c.1074T>C (p.Asp358=)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
312953NM_001099274.3(TINF2):c.507+5C>TTINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
38916NM_001099274.3(TINF2):c.734C>A (p.Ser245Tyr)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
662182NM_001099274.3(TINF2):c.1307C>T (p.Ala436Val)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
846888NM_001099274.3(TINF2):c.318G>C (p.Lys106Asn)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
880974NM_001099274.3(TINF2):c.253C>G (p.His85Asp)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
882334NM_001099274.3(TINF2):c.30A>G (p.Ala10=)TINF2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1422121NM_001099274.3(TINF2):c.166C>G (p.Arg56Gly)LOC130055403Uncertain significancecriteria provided, multiple submitters, no conflicts
1467172NM_001099274.3(TINF2):c.128C>A (p.Ala43Asp)LOC130055403Uncertain significancecriteria provided, multiple submitters, no conflicts
3001449NM_001099274.3(TINF2):c.73G>A (p.Gly25Arg)LOC130055403Uncertain significancecriteria provided, multiple submitters, no conflicts
3576546NM_001099274.3(TINF2):c.106G>A (p.Glu36Lys)LOC130055403Uncertain significancecriteria provided, multiple submitters, no conflicts
312960NM_001099274.3(TINF2):c.-93T>CLOC130055404Uncertain significancecriteria provided, single submitter
312963NM_001099274.3(TINF2):c.-223C>GLOC130055404Uncertain significancecriteria provided, single submitter
882601NM_001099274.3(TINF2):c.-130A>GLOC130055404Uncertain significancecriteria provided, single submitter
883384NM_001099274.3(TINF2):c.-233T>GLOC130055404Uncertain significancecriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 11 · Orphanet: 10 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
TINF2DefinitiveAutosomal dominantdyskeratosis congenita, autosomal dominant 311

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TINF2Orphanet:1775Dyskeratosis congenita
TINF2Orphanet:3088Revesz syndrome
TINF2Orphanet:3322Hoyeraal-Hreidarsson syndrome
TGM1Orphanet:100976Bathing suit ichthyosis
TGM1Orphanet:281122Self-improving collodion baby
TGM1Orphanet:281127Acral self-healing collodion baby
TGM1Orphanet:313Lamellar ichthyosis
TGM1Orphanet:79394Congenital ichthyosiform erythroderma
TNXBOrphanet:230839Classical-like Ehlers-Danlos syndrome type 1
TNXBOrphanet:289365Familial vesicoureteral reflux

Cohort genes → proteins

3 cohort genes, 3 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence3

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TINF2HGNC:11824ENSG00000092330Q9BSI4TERF1-interacting nuclear factor 2gencc,clinvar
TGM1HGNC:11777ENSG00000092295P22735Protein-glutamine gamma-glutamyltransferase Kclinvar
TNXBHGNC:11976ENSG00000168477P22105Tenascin-Xclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TINF2TERF1-interacting nuclear factor 2Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection.
TGM1Protein-glutamine gamma-glutamyltransferase KCatalyzes the cross-linking of proteins and the conjugation of polyamines to proteins.
TNXBTenascin-XAppears to mediate interactions between cells and the extracellular matrix.

Protein-family classification

Druggable: 2 · Difficult: 0 · Unknown: 1 · Druggable fraction: 0.67

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Antibody/Immunoglobulin219.5×0.007
Other/Unknown10.6×0.914

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TINF2Other/UnknownnoTINF2_N, TINF2
TGM1Antibody/Immunoglobulinyes2.3.2.13Transglutaminase_N, Transglutaminase-like, Transglutaminase_C
TNXBAntibody/ImmunoglobulinyesEGF, Fibrinogen_a/b/g_C_dom, FN3_dom

Expression context

Cohort genes with no expression data: 0.

3 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)3
unknown0

Top tissues across cohort

TissueCohort genes
right adrenal gland2
right adrenal gland cortex2
granulocyte1
esophagus mucosa1
lower esophagus mucosa1
skin of leg1
apex of heart1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TINF2144ubiquitousmarkergranulocyte, right adrenal gland, right adrenal gland cortex
TGM1135broadmarkerlower esophagus mucosa, esophagus mucosa, skin of leg
TNXB134ubiquitousmarkerapex of heart, right adrenal gland cortex, right adrenal gland

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
TGM11,978
TINF21,769
TNXB1,335

Structural data

PDB: 3 · AlphaFold-only: 0 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
TINF2Q9BSI43
TNXBP221053
TGM1P227351

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 19. Enrichment computed across 3 evidence-associated genes (3 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Telomere C-strand synthesis initiation1271.9×0.022TINF2
Processive synthesis on the C-strand of the telomere1253.8×0.022TINF2
Telomere C-strand (Lagging Strand) Synthesis1253.8×0.022TINF2
Removal of the Flap Intermediate from the C-strand1211.5×0.022TINF2
Telomere Extension By Telomerase1152.3×0.022TINF2
Polymerase switching on the C-strand of the telomere1141.0×0.022TINF2
Packaging Of Telomere Ends173.2×0.027TINF2
Recognition and association of DNA glycosylase with site containing an affected purine168.0×0.027TINF2
Cleavage of the damaged purine168.0×0.027TINF2
Recognition and association of DNA glycosylase with site containing an affected pyrimidine161.4×0.027TINF2
Cleavage of the damaged pyrimidine161.4×0.027TINF2
Inhibition of DNA recombination at telomere156.0×0.027TINF2
DNA Damage/Telomere Stress Induced Senescence154.4×0.027TINF2
ECM proteoglycans150.1×0.027TNXB
Meiotic synapsis147.0×0.027TINF2
Formation of the cornified envelope129.3×0.040TGM1
Extracellular matrix organization121.0×0.052TNXB
Keratinization118.6×0.056TGM1
Developmental Biology14.8×0.194TGM1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 3 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
regulation of telomere maintenance via telomere lengthening15617.3×0.003TINF2
positive regulation of cell fate determination15617.3×0.003TNXB
cell envelope organization11872.4×0.005TGM1
telomere assembly11404.3×0.005TINF2
positive regulation of collagen fibril organization11404.3×0.005TNXB
elastic fiber assembly1510.7×0.008TNXB
protein localization to chromosome, telomeric region1510.7×0.008TINF2
telomere capping1432.1×0.008TINF2
positive regulation of vascular endothelial growth factor signaling pathway1374.5×0.008TNXB
collagen metabolic process1351.1×0.008TNXB
cornification1351.1×0.008TGM1
positive regulation of keratinocyte proliferation1330.4×0.008TGM1
regulation of JNK cascade1295.6×0.008TNXB
negative regulation of telomere maintenance via telomerase1244.2×0.009TINF2
positive regulation of telomere maintenance1170.2×0.012TINF2
triglyceride metabolic process1147.8×0.012TNXB
positive regulation of cell cycle1147.8×0.012TGM1
regulation of cell differentiation1144.0×0.012TNXB
positive regulation of epithelial to mesenchymal transition1106.0×0.016TNXB
regulation of cell adhesion1102.1×0.016TNXB
negative regulation of epithelial cell proliferation196.8×0.016TINF2
keratinocyte differentiation182.6×0.017TGM1
protein modification process181.4×0.017TGM1
collagen fibril organization174.9×0.018TNXB
fatty acid metabolic process164.6×0.020TNXB
cell-matrix adhesion154.5×0.022TNXB
regulation of cell migration152.5×0.022TNXB
neuron projection development140.7×0.028TNXB
cell-cell adhesion133.8×0.032TNXB
actin cytoskeleton organization126.4×0.040TNXB

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 3

Druggability breadth: 1 of 3 evidence-associated genes (33%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

SymbolMoleculesMax phase
TINF200
TGM100
TNXB00

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
TGM111Binding:11

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
TGM12.3.2.13protein-glutamine gamma-glutamyltransferase

Pharmacogenomics

Cohort genes with a PharmGKB record: 3; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)0
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug2TGM1, TNXB
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug1TINF2

Undrugged target profiles

3 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
TINF20
TGM111
TNXB0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.