Familial sick sinus syndrome

disease
On this page

Also known as familial sinus node dysfunctionhereditary sick sinus syndromesick sinus syndrome 1, autosomal recessiveSSS1

Summary

Familial sick sinus syndrome (MONDO:0012061) is a disease with 9 cohort genes (6 GWAS associations across 2 studies).

At a glance

  • Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
  • Cohort genes: 9
  • GWAS associations: 6
  • ClinVar variants: 1

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Cases/families11WorldwideValidated
Point prevalence<1 / 1 000 000WorldwideValidated

Identifiers

Disease identifiers

FieldValue
Canonical namefamilial sick sinus syndrome
Mondo IDMONDO:0012061
MeSHC563907
OMIM608567
Orphanet166282
ICD-111495462959
SNOMED CT233913007
UMLSC0340491
MedGen573766
GARD0013663
MedDRA10040639
Is cancer (heuristic)no

Also known as: familial sinus node dysfunction · hereditary sick sinus syndrome · sick sinus syndrome 1, autosomal recessive · SSS1

Data availability: 1 ClinVar variant · 6 GWAS associations (2 studies) · 2 GenCC gene-disease records · 2 cell lines.

Disease family

An umbrella term covering 4 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › cardiovascular disorderheart disorderheart conduction diseasesinoatrial node disordersick sinus syndromefamilial sick sinus syndrome

Subtypes (4): sick sinus syndrome 2, autosomal dominant, sinus node disease and myopia, sick sinus syndrome 1, sick sinus syndrome 4

Genetics & variants

GWAS landscape

6 GWAS associations across 2 studies. Top hits map to 5 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs76897742e-15PITX2 - LINC01438T1.21
rs115544959e-14KRT8A1.62
rs129324458e-10ZFHX3C1.16
rs358138716e-09TTNA1.13
rs67959703e-08SCN10AA1.12
rs348838281e-07CCDC141A1.15

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST011360Thorolfsdottir RB20216,189931,046Genetic insight into sick sinus syndrome.
GCST001001Holm H201179237,592A rare variant in MYH6 is associated with high risk of sick sinus syndrome.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding4
Tier 2: splice/UTR0
Tier 3: regulatory0
Tier 4: intronic/intergenic2

MAF distribution

BucketVariants
common (>=0.05)5
low_freq (0.01-0.05)1
rare (<0.01)0
unknown0

Functional consequences

ConsequenceCount
missense_variant4
intergenic_variant1
intron_variant1

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs76897744110782354G>T0.201intergenic_variantPITX2 - LINC014382e-15Tier 4: intronic/intergenic
rs115544951252904798C>A,G,T0.016missense_variantKRT89e-14Tier 1: coding
rs129324451673035989T>C0.201intron_variantZFHX38e-10Tier 4: intronic/intergenic
rs358138712178785681G>A0.266missense_variantTTN6e-09Tier 1: coding
rs6795970338725184A>G,T0.358missense_variantSCN10A3e-08Tier 1: coding
rs348838282178905448C>A,T0.152missense_variantCCDC1411e-07Tier 1: coding

ClinVar germline variants

1 retrieved; paginated sample, class counts are floors:

1 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
1348900NM_000335.5(SCN5A):c.999-1G>ASCN5ALikely pathogeniccriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 31 · Orphanet: 36 · 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
HCN4StrongAutosomal dominantsick sinus syndrome 2, autosomal dominant8
SCN5AStrongAutosomal recessivesick sinus syndrome 123

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
SCN5AOrphanet:101016Romano-Ward syndrome
SCN5AOrphanet:130Brugada syndrome
SCN5AOrphanet:1344Isolated atrial standstill
SCN5AOrphanet:154Familial isolated dilated cardiomyopathy
SCN5AOrphanet:166282Hereditary sick sinus syndrome
SCN5AOrphanet:228140Idiopathic ventricular fibrillation
SCN5AOrphanet:334Hereditary atrial fibrillation
SCN5AOrphanet:871Hereditary progressive cardiac conduction defect
HCN4Orphanet:130Brugada syndrome
HCN4Orphanet:166282Hereditary sick sinus syndrome
SCN10AOrphanet:101016Romano-Ward syndrome
SCN10AOrphanet:130Brugada syndrome
SCN10AOrphanet:306577Hereditary sodium channelopathy-related small fibers neuropathy
SCN10AOrphanet:46348Paroxysmal extreme pain disorder
SCN10AOrphanet:88642Congenital insensitivity to pain-anosmia-neuropathic arthropathy
SCN10AOrphanet:90026Primary erythromelalgia
TTNOrphanet:140922Titin-related limb-girdle muscular dystrophy R10
TTNOrphanet:154Familial isolated dilated cardiomyopathy
TTNOrphanet:169186Autosomal recessive centronuclear myopathy
TTNOrphanet:178464Hereditary myopathy with early respiratory failure
TTNOrphanet:289377Early-onset myopathy with fatal cardiomyopathy
TTNOrphanet:293888Inherited isolated arrhythmogenic cardiomyopathy, dominant-left variant
TTNOrphanet:293899Inherited isolated arrhythmogenic ventricular dysplasia, biventricular variant
TTNOrphanet:293910Inherited isolated arrhythmogenic cardiomyopathy, dominant-right variant
TTNOrphanet:324604Classic multiminicore myopathy
TTNOrphanet:334Hereditary atrial fibrillation
TTNOrphanet:466921Childhood-onset progressive contractures-limb-girdle weakness-muscle dystrophy syndrome
TTNOrphanet:609Tibial muscular dystrophy
TTNOrphanet:707983Early-onset autosomal recessive TTN-related distal myopathy
CCDC141Orphanet:478Kallmann syndrome
PITX2Orphanet:334Hereditary atrial fibrillation
PITX2Orphanet:708Peters anomaly
PITX2Orphanet:782Axenfeld-Rieger syndrome
PITX2Orphanet:91481Ring dermoid of cornea
PITX2Orphanet:91483Rieger anomaly
PITX2Orphanet:98978Axenfeld anomaly

Cohort genes → proteins

9 cohort genes, 8 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only7
multi_evidence2

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
SCN5AHGNC:10593ENSG00000183873Q14524Sodium channel protein type 5 subunit alphagencc,clinvar
HCN4HGNC:16882ENSG00000138622Q9Y3Q4Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4gencc
SCN10AHGNC:10582ENSG00000185313Q9Y5Y9Sodium channel protein type 10 subunit alphagwas
TTNHGNC:12403ENSG00000155657Q8WZ42Titingwas
CCDC141HGNC:26821ENSG00000163492Q6ZP82Coiled-coil domain-containing protein 141gwas
MIR297HGNC:33691ENSG00000215961microRNA 297gwas
KRT8HGNC:6446ENSG00000170421P05787Keratin, type II cytoskeletal 8gwas
ZFHX3HGNC:777ENSG00000140836Q15911Zinc finger homeobox protein 3gwas
PITX2HGNC:9005ENSG00000164093Q99697Pituitary homeobox 2gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
SCN5ASodium channel protein type 5 subunit alphaPore-forming subunit of Nav1.5, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes.
HCN4Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 4Hyperpolarization-activated ion channel that are permeable to Na(+) and K(+) ions with very slow activation and inactivation.
SCN10ASodium channel protein type 10 subunit alphaTetrodotoxin-resistant channel that mediates the voltage-dependent sodium ion permeability of excitable membranes.
TTNTitinKey component in the assembly and functioning of vertebrate striated muscles.
CCDC141Coiled-coil domain-containing protein 141Plays a critical role in cortical radial and GnRH neurons migration during brain development.
KRT8Keratin, type II cytoskeletal 8Required for the formation of KRT8/KRT18 filaments that are involved in ARHGEF40-mediated actin stress fiber formation and tensional force-induced stress fiber formation and reinforcement.
ZFHX3Zinc finger homeobox protein 3Transcriptional regulator which can act as an activator or a repressor.
PITX2Pituitary homeobox 2May play a role in myoblast differentiation.

Protein-family classification

Druggable: 5 · Difficult: 2 · Unknown: 2 · Druggable fraction: 0.56

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 channel337.2×3e-04
Antibody/Immunoglobulin13.2×0.374
Kinase13.1×0.374
Transcription factor21.8×0.374
Other/Unknown20.4×0.992

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
SCN5AIon channelyesNa_channel_asu, Ion_trans_dom, Na_channel_a5su
HCN4Ion channelyescNMP-bd_dom, K_chnl_volt-dep_EAG/ELK/ERG, Ion_trans_dom
SCN10AIon channelyesNa_channel_asu, Ion_trans_dom, Na_trans_assoc_dom
TTNKinaseyes2.7.11.1Prot_kinase_dom, Ig_sub2, Ig_sub
CCDC141Antibody/ImmunoglobulinyesSpectrin_repeat, Ig_sub2, Ig_sub
MIR297Other/Unknownno
KRT8Other/UnknownnoKeratin_II, IF_conserved, Keratin_2_head
ZFHX3Transcription factornoHD, Matrin/U1-like-C_Znf_C2H2, Homeodomain-like_sf
PITX2Transcription factornoHD, OAR_dom, Homeodomain-like_sf

Expression context

Cohort genes with no expression data: 0.

6 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)9
unknown0

Top tissues across cohort

TissueCohort genes
heart left ventricle2
right atrium auricular region2
biceps brachii2
apex of heart1
cardiac ventricle1
cardiac atrium1
tibialis anterior1
diaphragm1
olfactory bulb1
type B pancreatic cell1
gluteal muscle1
skeletal muscle tissue of biceps brachii1
adrenal tissue1
endometrium1
gastrocnemius1
monocyte1
duodenum1
endometrium epithelium1
mucosa of transverse colon1
buccal mucosa cell1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
SCN5A161broadyesapex of heart, heart left ventricle, cardiac ventricle
HCN486tissue_specificyestibialis anterior, right atrium auricular region, cardiac atrium
SCN10A21markertype B pancreatic cell, olfactory bulb, diaphragm
TTN223broadmarkerbiceps brachii, gluteal muscle, skeletal muscle tissue of biceps brachii
CCDC141149broadmarkerheart left ventricle, adrenal tissue, right atrium auricular region
MIR29738yesendometrium, gastrocnemius, monocyte
KRT8159ubiquitousmarkermucosa of transverse colon, endometrium epithelium, duodenum
ZFHX3274ubiquitousmarkersaphenous vein, buccal mucosa cell, synovial joint
PITX2166broadmarkergingiva, biceps brachii, gingival epithelium

Protein interactions among cohort

Intra-cohort edges: 3.

Hub genes (top 10 by interactor count)

SymbolInteractor count
TTN4,237
KRT83,915
PITX22,389
SCN5A2,090
SCN10A1,802
ZFHX31,649
HCN41,279
CCDC1411,255
MIR2970

Intra-cohort edges

ABSources
HCN4PITX2string_interaction
HCN4SCN5Astring_interaction
PITX2ZFHX3string_interaction

Structural data

PDB: 7 · AlphaFold-only: 1 · No structure: 1

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
TTNQ8WZ4264
SCN5AQ1452416
HCN4Q9Y3Q48
SCN10AQ9Y5Y98
KRT8P057873
ZFHX3Q159113
PITX2Q996973

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
CCDC141Q6ZP8272.36

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 17. Enrichment computed across 9 evidence-associated genes (7 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 7 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Interaction between L1 and Ankyrins2105.2×0.001SCN5A, SCN10A
Phase 0 - rapid depolarisation298.9×0.001SCN5A, SCN10A
HCN channels1407.9×0.007HCN4
TFAP2 (AP-2) family regulates transcription of other transcription factors1407.9×0.007PITX2
L1CAM interactions234.4×0.007SCN5A, SCN10A
Cardiac conduction231.1×0.007SCN5A, SCN10A
Muscle contraction222.1×0.008SCN5A, SCN10A
RUNX3 regulates CDKN1A transcription1233.1×0.009ZFHX3
Developmental Lineage of Mammary Gland Alveolar Cells190.6×0.016KRT8
Axon guidance212.9×0.016SCN5A, SCN10A
Nervous system development212.3×0.016SCN5A, SCN10A
Developmental Biology36.2×0.016SCN5A, SCN10A, KRT8
Developmental Lineage of Mammary Gland Luminal Epithelial Cells165.3×0.020KRT8
Striated Muscle Contraction144.1×0.027TTN
Platelet degranulation112.6×0.082TTN
Formation of the cornified envelope112.6×0.082KRT8
Keratinization18.0×0.119KRT8

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 8 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
bundle of His cell action potential22106.5×3e-05SCN5A, SCN10A
regulation of heart rate3175.5×3e-05SCN5A, SCN10A, HCN4
AV node cell action potential21053.2×5e-05SCN5A, SCN10A
membrane depolarization during SA node cell action potential2842.6×6e-05SCN5A, HCN4
SA node cell action potential2702.2×8e-05SCN5A, HCN4
regulation of atrial cardiac muscle cell membrane depolarization2468.1×1e-04SCN5A, SCN10A
sodium ion transmembrane transport376.1×1e-04SCN5A, SCN10A, HCN4
membrane depolarization during action potential2421.3×1e-04SCN5A, SCN10A
membrane depolarization during cardiac muscle cell action potential2351.1×2e-04SCN5A, HCN4
regulation of cardiac muscle contraction2221.7×4e-04SCN10A, HCN4
cardiac muscle cell action potential involved in contraction2175.5×6e-04SCN5A, SCN10A
cardiac muscle contraction2100.3×0.002SCN5A, TTN
regulation of heart rate by cardiac conduction293.6×0.002SCN5A, HCN4
odontogenesis of dentin-containing tooth275.2×0.003SCN5A, SCN10A
subthalamic nucleus development12106.5×0.004PITX2
superior vena cava morphogenesis12106.5×0.004PITX2
muscle contraction252.0×0.005TTN, HCN4
hypothalamus cell migration11053.2×0.005PITX2
prolactin secreting cell differentiation11053.2×0.005PITX2
left lung morphogenesis11053.2×0.005PITX2
pulmonary vein morphogenesis11053.2×0.005PITX2
cell proliferation involved in outflow tract morphogenesis11053.2×0.005PITX2
AV node cell to bundle of His cell communication11053.2×0.005SCN5A
regulation of locomotor rhythm11053.2×0.005ZFHX3
pulmonary myocardium development1702.2×0.005PITX2
skeletal muscle myosin thick filament assembly1702.2×0.005TTN
vascular associated smooth muscle cell differentiation1702.2×0.005PITX2
deltoid tuberosity development1702.2×0.005PITX2
sarcomerogenesis1702.2×0.005TTN
response to other organism1702.2×0.005KRT8

Therapeutics

Drug target analysis

Approved (phase 4): 3 · Phase ≥3: 3 · Phased (≥1): 3 · Undrugged: 6

Druggability breadth: 4 of 9 evidence-associated genes (44%) 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
SCN5ABEPRIDIL
HCN4IVABRADINE
SCN10AIMIPRAMINE

Top cohort targets by molecule count

SymbolMoleculesMax phase
SCN5A1084
SCN10A214
HCN424
TTN00
CCDC14100
MIR29700
KRT800
ZFHX300
PITX200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BEPRIDIL4SCN5A
CANDESARTAN CILEXETIL4SCN5A
TELMISARTAN4SCN5A
CARBAMAZEPINE4SCN5A
DIBUCAINE4SCN5A
IMIPRAMINE4SCN10A, SCN5A
DROPERIDOL4SCN5A
PONATINIB4SCN5A
DULOXETINE4SCN5A
PALONOSETRON4SCN5A
VILANTEROL4SCN5A
MEXILETINE HYDROCHLORIDE4SCN5A
UNOPROSTONE ISOPROPYL4SCN5A
LURASIDONE4SCN5A
LETERMOVIR4SCN5A
SERTINDOLE4SCN10A, SCN5A
FEDRATINIB4SCN5A
QUINIDINE4SCN5A
DARUNAVIR4SCN5A
DARIFENACIN4SCN5A
BENZONATATE4SCN5A
TOLTERODINE4SCN5A
RANOLAZINE4SCN5A
PIMOZIDE4SCN10A, SCN5A
NIMODIPINE4SCN5A
FELODIPINE4SCN5A
NICARDIPINE4SCN5A
AMLODIPINE4SCN5A
PHENYTOIN4SCN5A
PALIPERIDONE4SCN5A

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

SymbolAssaysType breakdown
SCN5A594Binding:380, Functional:98, ADMET:72, Toxicity:43, Unclassified:1
SCN10A144Binding:124, Functional:16, ADMET:4
HCN430Binding:20, ADMET:5, Functional:4, Toxicity:1
TTN1Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
TTN2.7.11.1non-specific serine/threonine protein kinase

Cohort genes with high screening signal

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

SymbolChEMBL assays
SCN5A594
SCN10A144

Pharmacogenomics

Cohort genes with a PharmGKB record: 9; 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)
BEPRIDIL4SCN5A
CANDESARTAN CILEXETIL4SCN5A
TELMISARTAN4SCN5A
CARBAMAZEPINE4SCN5A
DIBUCAINE4SCN5A
IMIPRAMINE4SCN10A, SCN5A
DROPERIDOL4SCN5A
PONATINIB4SCN5A
DULOXETINE4SCN5A
PALONOSETRON4SCN5A
VILANTEROL4SCN5A
MEXILETINE HYDROCHLORIDE4SCN5A
UNOPROSTONE ISOPROPYL4SCN5A
LURASIDONE4SCN5A
LETERMOVIR4SCN5A
SERTINDOLE4SCN10A, SCN5A
FEDRATINIB4SCN5A
QUINIDINE4SCN5A
DARUNAVIR4SCN5A
DARIFENACIN4SCN5A
BENZONATATE4SCN5A
TOLTERODINE4SCN5A
RANOLAZINE4SCN5A
PIMOZIDE4SCN10A, SCN5A
NIMODIPINE4SCN5A
FELODIPINE4SCN5A
NICARDIPINE4SCN5A
AMLODIPINE4SCN5A
PHENYTOIN4SCN5A
PALIPERIDONE4SCN5A

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3SCN5A, HCN4, SCN10A
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1TTN
DDruggable family + AlphaFold only, no drug1CCDC141
EDifficult family or no structure, no drug4MIR297, KRT8, ZFHX3, PITX2

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
TTN1
CCDC1410
MIR2970
KRT80
ZFHX30
PITX20

Clinical trials & evidence

Clinical trials

Clinical trials: 0.