pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3

disease
On this page

Also known as PFBMFT3pulmonary fibrosis and/or bone marrow failure, Telomere-related caused by mutation in RTEL1pulmonary fibrosis and/or bone marrow failure, Telomere-related, type 3RTEL1 pulmonary fibrosis and/or bone marrow failure, Telomere-related

Summary

pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 (MONDO:0014613) is a disease caused by RTEL1 (GenCC Definitive), with 5 cohort genes.

At a glance

  • Causal gene: RTEL1 (GenCC Definitive)
  • Cohort genes: 5
  • ClinVar variants: 3,395

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namepulmonary fibrosis and/or bone marrow failure, Telomere-related, 3
Mondo IDMONDO:0014613
OMIM616373
UMLSC4225346
MedGen901644
GARD0016098
Is cancer (heuristic)no

Also known as: PFBMFT3 · pulmonary fibrosis and/or bone marrow failure, Telomere-related caused by mutation in RTEL1 · pulmonary fibrosis and/or bone marrow failure, Telomere-related, 3 · pulmonary fibrosis and/or bone marrow failure, Telomere-related, type 3 · RTEL1 pulmonary fibrosis and/or bone marrow failure, Telomere-related

Data availability: 3,395 ClinVar variants · 4 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › respiratory system disorderlower respiratory tract disorderlung disorderinterstitial lung diseasepulmonary fibrosispulmonary fibrosis and/or bone marrow failure, telomere-relatedpulmonary fibrosis and/or bone marrow failure, Telomere-related, 3

Related subtypes (8): pulmonary fibrosis and/or bone marrow failure, Telomere-related, 1, pulmonary fibrosis and/or bone marrow failure, Telomere-related, 2, pulmonary fibrosis and/or bone marrow failure, Telomere-related, 4, pulmonary fibrosis and/or bone marrow failure, telomere-related, 6, pulmonary fibrosis and/or bone marrow failure, telomere-related, 5, pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 7, pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 8, pulmonary fibrosis and/or bone marrow failure syndrome, telomere-related, 9

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

600 retrieved; paginated sample, class counts are floors:

387 likely benign, 148 uncertain significance, 18 pathogenic, 16 benign, 14 conflicting classifications of pathogenicity, 6 likely pathogenic, 6 pathogenic/likely pathogenic, 5 benign/likely benign

ClinVarVariant (HGVS)GeneClassificationReview
1048767NM_001283009.2(RTEL1):c.9del (p.Lys3_Ile4insTer)RTEL1Pathogeniccriteria provided, single submitter
1068424NM_001283009.2(RTEL1):c.1236_1266+47delRTEL1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1069534NM_001283009.2(RTEL1):c.1603G>T (p.Glu535Ter)RTEL1Pathogeniccriteria provided, single submitter
1069734NM_001283009.2(RTEL1):c.2098del (p.Arg700fs)RTEL1Pathogeniccriteria provided, single submitter
1070371NM_001283009.2(RTEL1):c.3043C>T (p.Gln1015Ter)RTEL1Pathogeniccriteria provided, single submitter
1071073NM_001283009.2(RTEL1):c.1458del (p.Ser487fs)RTEL1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1071517NC_000020.10:g.(?62290746)(62290867_?)delRTEL1Pathogeniccriteria provided, single submitter
1071518NC_000020.10:g.(?62298812)(62298916_?)delRTEL1Pathogeniccriteria provided, single submitter
1071780NM_001283009.2(RTEL1):c.2653G>T (p.Glu885Ter)RTEL1Pathogeniccriteria provided, single submitter
1071913NM_001283009.2(RTEL1):c.3766C>T (p.Gln1256Ter)RTEL1Pathogeniccriteria provided, single submitter
1072324NM_001283009.2(RTEL1):c.329_332del (p.Ile110fs)RTEL1Pathogeniccriteria provided, single submitter
1072371NM_001283009.2(RTEL1):c.3074_3096del (p.Gly1025fs)RTEL1Pathogeniccriteria provided, single submitter
1073438NC_000020.10:g.(?62290746)(62312082_?)delRTEL1Pathogeniccriteria provided, single submitter
1075174NM_001283009.2(RTEL1):c.3553del (p.Arg1186fs)RTEL1Pathogeniccriteria provided, single submitter
1076662NM_001283009.2(RTEL1):c.3138del (p.Ser1047fs)RTEL1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1076689NM_001283009.2(RTEL1):c.2554C>T (p.Gln852Ter)RTEL1Pathogeniccriteria provided, multiple submitters, no conflicts
1076873NM_001283009.2(RTEL1):c.1194del (p.Ile398fs)RTEL1Pathogeniccriteria provided, single submitter
1325019NM_001283009.2(RTEL1):c.2821G>T (p.Glu941Ter)RTEL1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1342130NM_001283009.2(RTEL1):c.3109+1G>CRTEL1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1358040NM_001283009.2(RTEL1):c.1890dup (p.Leu631fs)RTEL1Pathogeniccriteria provided, single submitter
1361216NC_000020.10:g.(?62298812)(62303984_?)delRTEL1Pathogeniccriteria provided, single submitter
1364279NM_001283009.2(RTEL1):c.2584_2593del (p.Leu862fs)RTEL1Pathogeniccriteria provided, single submitter
1338484NM_001283009.2(RTEL1):c.190C>T (p.Arg64Ter)RTEL1-TNFRSF6BPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1350840NM_001283009.2(RTEL1):c.46C>T (p.Gln16Ter)RTEL1-TNFRSF6BPathogeniccriteria provided, single submitter
1066098NC_000020.10:g.(?62292641)(62327221_?)delRTEL1Likely pathogeniccriteria provided, single submitter
1066573NM_001283009.2(RTEL1):c.1191+1G>ARTEL1Likely pathogeniccriteria provided, single submitter
1066646NM_001283009.2(RTEL1):c.3343+1G>CRTEL1Likely pathogeniccriteria provided, single submitter
1066945NM_001283009.2(RTEL1):c.1266+2T>GRTEL1Likely pathogeniccriteria provided, single submitter
1067185NM_001283009.2(RTEL1):c.2265+1G>TRTEL1Likely pathogeniccriteria provided, multiple submitters, no conflicts
1068395NM_001283009.2(RTEL1):c.3787del (p.Gln1263fs)RTEL1-TNFRSF6BLikely pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 12 · Orphanet: 14 · 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
RTEL1DefinitiveSemidominantpulmonary fibrosis and/or bone marrow failure, Telomere-related, 312

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
RTEL1Orphanet:1775Dyskeratosis congenita
RTEL1Orphanet:2032Idiopathic pulmonary fibrosis
RTEL1Orphanet:3322Hoyeraal-Hreidarsson syndrome
SCN2AOrphanet:140927Self-limited neonatal-infantile epilepsy
SCN2AOrphanet:1934Early infantile developmental and epileptic encephalopathy
SCN2AOrphanet:2131Alternating hemiplegia of childhood
SCN2AOrphanet:293181Epilepsy of infancy with migrating focal seizures
SCN2AOrphanet:306Self-limited infantile epilepsy
SCN2AOrphanet:33069Dravet syndrome
SCN2AOrphanet:36387Genetic epilepsy with febrile seizure plus
SCN2AOrphanet:697160Infantile epileptic spasms syndrome
CHRNA4Orphanet:98784Sleep-related hypermotor epilepsy
EEF1A2Orphanet:178469Autosomal dominant non-syndromic intellectual disability
EEF1A2Orphanet:442835Non-specific early-onset epileptic encephalopathy

Cohort genes → proteins

5 cohort genes, 4 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence5

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
RTEL1HGNC:15888ENSG00000258366Q9NZ71Regulator of telomere elongation helicase 1gencc,clinvar
SCN2AHGNC:10588ENSG00000136531Q99250Sodium channel protein type 2 subunit alphaclinvar
CHRNA4HGNC:1958ENSG00000101204P43681Neuronal acetylcholine receptor subunit alpha-4clinvar
EEF1A2HGNC:3192ENSG00000101210Q05639Elongation factor 1-alpha 2clinvar
RTEL1-TNFRSF6BHGNC:44095ENSG00000026036RTEL1-TNFRSF6B readthrough (NMD candidate)clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
RTEL1Regulator of telomere elongation helicase 1A probable ATP-dependent DNA helicase implicated in telomere-length regulation, DNA repair and the maintenance of genomic stability.
SCN2ASodium channel protein type 2 subunit alphaMediates the voltage-dependent sodium ion permeability of excitable membranes.
CHRNA4Neuronal acetylcholine receptor subunit alpha-4Component of neuronal acetylcholine receptors (nAChRs) that function as pentameric, ligand-gated cation channels with high calcium permeability among other activities. nAChRs are excitatory neurotrasnmitter receptors formed by a collection…
EEF1A2Elongation factor 1-alpha 2Translation elongation factor that catalyzes the GTP-dependent binding of aminoacyl-tRNA (aa-tRNA) to the A-site of ribosomes during the elongation phase of protein synthesis.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 4 · Druggable fraction: 0.2

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
Ion channel122.3×0.088
Other/Unknown41.4×0.269

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
RTEL1Other/UnknownnoHelicase-like_DEXD_c2, ATP-dep_Helicase_C, RAD3-like_helicase_DEAD
SCN2AIon channelyesIQ_motif_EF-hand-BS, Na_channel_asu, Ion_trans_dom
CHRNA4Other/UnknownnoNicotinic_acetylcholine_rcpt, Neurotrans-gated_channel_TM, Neur_channel
EEF1A2Other/UnknownnoT_Tr_GTP-bd_dom, EFTu-like_2, Transl_elong_EF1A_euk/arc
RTEL1-TNFRSF6BOther/Unknownno

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)5
unknown0

Top tissues across cohort

TissueCohort genes
cerebellar hemisphere2
right hemisphere of cerebellum2
sural nerve1
Brodmann (1909) area 231
cerebellar vermis1
middle temporal gyrus1
cingulate cortex1
cortical plate1
right lobe of liver1
apex of heart1
gastrocnemius1
hindlimb stylopod muscle1
cerebellum1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
RTEL1134ubiquitousyessural nerve, right hemisphere of cerebellum, cerebellar hemisphere
SCN2A187broadmarkermiddle temporal gyrus, Brodmann (1909) area 23, cerebellar vermis
CHRNA4138tissue_specificyesright lobe of liver, cortical plate, cingulate cortex
EEF1A2247ubiquitousmarkergastrocnemius, apex of heart, hindlimb stylopod muscle
RTEL1-TNFRSF6B135markerright hemisphere of cerebellum, cerebellar hemisphere, cerebellum

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

SymbolInteractor count
SCN2A2,810
RTEL12,324
CHRNA41,989
EEF1A2745
RTEL1-TNFRSF6B0

Structural data

PDB: 4 · AlphaFold-only: 0 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
CHRNA4P4368112
SCN2AQ992505
RTEL1Q9NZ713
EEF1A2Q056392

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 35. Enrichment computed across 5 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Highly sodium permeable postsynaptic acetylcholine nicotinic receptors1407.9×0.026CHRNA4
Highly calcium permeable nicotinic acetylcholine receptors1317.2×0.026CHRNA4
Highly calcium permeable postsynaptic nicotinic acetylcholine receptors1259.6×0.026CHRNA4
Presynaptic nicotinic acetylcholine receptors1237.9×0.026CHRNA4
Acetylcholine binding and downstream events1203.9×0.026CHRNA4
Postsynaptic nicotinic acetylcholine receptors1203.9×0.026CHRNA4
Cytosolic iron-sulfur cluster assembly1190.3×0.026RTEL1
Resolution of D-Loop Structures1158.6×0.026RTEL1
Extension of Telomeres1150.3×0.026RTEL1
Telomere Extension By Telomerase1114.2×0.026RTEL1
Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)198.5×0.026RTEL1
Telomere Maintenance192.1×0.026RTEL1
Interaction between L1 and Ankyrins192.1×0.026SCN2A
Phase 0 - rapid depolarisation186.5×0.026SCN2A
Sensory perception of taste184.0×0.026SCN2A
Homology Directed Repair177.2×0.026RTEL1
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)177.2×0.026RTEL1
Eukaryotic Translation Elongation169.6×0.026EEF1A2
Sensory perception of sweet, bitter, and umami (glutamate) taste169.6×0.026SCN2A
DNA Double-Strand Break Repair162.1×0.028RTEL1
Chromosome Maintenance152.9×0.031RTEL1
HDR through Homologous Recombination (HRR)147.6×0.033RTEL1
L1CAM interactions130.1×0.050SCN2A
Cardiac conduction127.2×0.053SCN2A
Neurotransmitter receptors and postsynaptic signal transmission125.0×0.054CHRNA4
DNA Repair124.6×0.054RTEL1
Sensory Perception123.8×0.054SCN2A
Muscle contraction119.3×0.062SCN2A
Transmission across Chemical Synapses119.0×0.062CHRNA4
Axon guidance111.3×0.098SCN2A

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
DNA strand displacement14213.0×0.003RTEL1
positive regulation of lipid kinase activity14213.0×0.003EEF1A2
negative regulation of telomere maintenance in response to DNA damage14213.0×0.003RTEL1
positive regulation of telomeric loop disassembly14213.0×0.003RTEL1
intrinsic apoptotic signaling pathway in response to osmotic stress12106.5×0.004SCN2A
telomeric loop disassembly12106.5×0.004RTEL1
mitotic telomere maintenance via semi-conservative replication11404.3×0.005RTEL1
negative regulation of t-circle formation11404.3×0.005RTEL1
positive regulation of telomere capping1842.6×0.006RTEL1
regulation of chaperone-mediated autophagy1842.6×0.006EEF1A2
positive regulation of telomere maintenance via telomere lengthening1702.2×0.006RTEL1
DNA repair231.9×0.006RTEL1, CHRNA4
behavioral response to nicotine1468.1×0.008CHRNA4
telomere maintenance in response to DNA damage1468.1×0.008RTEL1
inhibitory postsynaptic potential1421.3×0.008CHRNA4
translational elongation1300.9×0.010EEF1A2
regulation of dopamine secretion1300.9×0.010CHRNA4
nervous system process1300.9×0.010CHRNA4
negative regulation of DNA recombination1280.9×0.010RTEL1
regulation of double-strand break repair via homologous recombination1247.8×0.010RTEL1
synaptic transmission, cholinergic1200.6×0.012CHRNA4
cardiac muscle cell action potential involved in contraction1175.5×0.013SCN2A
acetylcholine receptor signaling pathway1156.0×0.014CHRNA4
neuromuscular synaptic transmission1150.5×0.014CHRNA4
positive regulation of telomere maintenance1127.7×0.016RTEL1
membrane depolarization1127.7×0.016CHRNA4
neuronal action potential1120.4×0.016SCN2A
B cell activation1113.9×0.016CHRNA4
presynaptic modulation of chemical synaptic transmission1113.9×0.016CHRNA4
replication fork processing1105.3×0.016RTEL1

Therapeutics

Drug target analysis

Approved (phase 4): 2 · Phase ≥3: 2 · Phased (≥1): 2 · Undrugged: 3

Druggability breadth: 3 of 5 evidence-associated genes (60%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
SCN2ABEPRIDIL
CHRNA4VARENICLINE

Top cohort targets by molecule count

SymbolMoleculesMax phase
SCN2A994
CHRNA4644
RTEL100
EEF1A200
RTEL1-TNFRSF6B00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BEPRIDIL4SCN2A
DIBUCAINE4SCN2A
ARTICAINE4SCN2A
BUPIVACAINE4SCN2A
IMIPRAMINE4SCN2A
DROPERIDOL4SCN2A
DICYCLOMINE4SCN2A
TETRABENAZINE4SCN2A
PHENIRAMINE4SCN2A
PRILOCAINE4SCN2A
PROPOXYCAINE4SCN2A
PROPARACAINE4SCN2A
HEXYLCAINE4SCN2A
PRAMOXINE4SCN2A
BENOXINATE4SCN2A
QUINIDINE4SCN2A
FELODIPINE4SCN2A
PHENYTOIN4SCN2A
QUININE4SCN2A
NISOLDIPINE4SCN2A
NIFEDIPINE4SCN2A
PRAZOSIN4SCN2A
DILTIAZEM4SCN2A
PRENYLAMINE4SCN2A
COCAINE4SCN2A
TRIFLUOPERAZINE4SCN2A
CINNARIZINE4SCN2A
THIORIDAZINE4CHRNA4, SCN2A
ETIDOCAINE4SCN2A
CHLORPHENIRAMINE4SCN2A

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

SymbolAssaysType breakdown
CHRNA4624Binding:497, Functional:125, Toxicity:1, ADMET:1
SCN2A203Binding:172, Functional:20, ADMET:10, Toxicity:1
EEF1A28Binding:8

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
SCN2A203
CHRNA4624

Pharmacogenomics

Cohort genes with a PharmGKB record: 4; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

30 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.

CompoundMax phaseCohort target (bioactivity)
BEPRIDIL4SCN2A
DIBUCAINE4SCN2A
ARTICAINE4SCN2A
BUPIVACAINE4SCN2A
IMIPRAMINE4SCN2A
DROPERIDOL4SCN2A
DICYCLOMINE4SCN2A
TETRABENAZINE4SCN2A
PHENIRAMINE4SCN2A
PRILOCAINE4SCN2A
PROPOXYCAINE4SCN2A
PROPARACAINE4SCN2A
HEXYLCAINE4SCN2A
PRAMOXINE4SCN2A
BENOXINATE4SCN2A
QUINIDINE4SCN2A
FELODIPINE4SCN2A
PHENYTOIN4SCN2A
QUININE4SCN2A
NISOLDIPINE4SCN2A
NIFEDIPINE4SCN2A
PRAZOSIN4SCN2A
DILTIAZEM4SCN2A
PRENYLAMINE4SCN2A
COCAINE4SCN2A
TRIFLUOPERAZINE4SCN2A
CINNARIZINE4SCN2A
THIORIDAZINE4CHRNA4, SCN2A
ETIDOCAINE4SCN2A
CHLORPHENIRAMINE4SCN2A

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)2SCN2A, CHRNA4
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug3RTEL1, EEF1A2, RTEL1-TNFRSF6B

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
RTEL10
EEF1A28
RTEL1-TNFRSF6B0

Clinical trials & evidence

Clinical trials

Clinical trials: 0.