1. Classification by unit size

  • STR (microsatellites): 1-6 bp → thickness of neurological pathology
  • VNTR (broad sense): variable number of copies, largest unit
  • Classic minisatellites: 10-60 bp (INS, MUC1)
  • Macrosatellites: thousands of bp — same principle (variable number of copies), much larger unit (FSHD/D4Z4)

2. Why they are unstable (common mechanism)

  • DNA polymerase slippage during replication
  • Nascent strand dissociates and reassociates in displaced register → loop
  • Loop in nascent strand → expansion
  • Mold strand loop → contraction
  • The greater the prior length, the greater the probability of loop → nonlinear instability after critical threshold (normal → premutation → complete mutation)

Clinical consequence: genetic anticipation = phenotypic manifestation of this increasing meiotic instability (paternal or maternal bias depending on the disease).

3. Three mechanisms depending on the location of the repeat (STR block)

A) Coding exon, triplets (CAG=polyQ)

  • Abnormal protein with polyglutamine tract
  • Misfolding → intranuclear aggregation
  • Toxic gain of function, dominant
  • Ex: Huntington, SCAs, Kennedy (X-linked)

B) Non-coding region (UTR, intron), large expansion

  • Epigenetic silencing → hypermethylation → loss of function (Fragile X, Friedreich)
  • RNA toxicity → sequestration of splicing proteins by messenger RNA with expanded repeat (myotonic, C9orf72)
Neurological diseases caused by STRs.
Abbreviated phenotype (MIM number)GeneMode of inheritanceRepeat MotifLocation on GenePathogenic repeat numberaChromosomeCoordinates (hg38)Clinical phenotypeReferences
C9-FTD
C9-ALS
(#10550)		C9orf72ADGGGGCC5’ Region24–4000chr92757348527573546Frontotemporal dementia, amyotrophic lateral sclerosis[32, 47, 65]
CANVAS
(#614575)		RFC1AR(AAGGG)400–2000
(ACAGG)exp
AAAAG (normal)		Intron 2400–2000chr43934842539348483Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome[11, 28, 138]
DM1
(#160900)		DMPKADCTG
(Interruptions: CCG)		3’ Region50–10,000chr194577020545770266Myotonic dystrophy 1[60, 176]
DM2
(#602668)		CNBP (ZNF9)ADCCTGIntron 150–11,000chr3129172577129172656Myotonic dystrophy 2[176]
DRPLA
(#125370)		ATN1ADCAGExon 549–93chr1269367176936775Dentatorubral-pallidoluysian atrophy[78]
EIEE1/XLID
(#308350)
(#300419)
(#300215)		ARXXLGCCExon 217–27chrX2501365425013697Clinical spectrum of disorders including developmental and epileptic encephalopathy 1, hydranencephaly with abnormal genitalia, X-linked lissencephaly 2 and X-linked mental retardation 29[73, 150]
FAME1 (#601068)SAMD12ADTTTCA
within TTTTA repeat region		Intron 4105–3680chr8118366813118366918Familial adult myoclonic epilepsy 1[22, 68]
FAME2
(#607876)		STARD7ADATTTC
within ATTTT repeat region		Intron 1150–460chr29619706796197124Familial adult myoclonic epilepsy 2[27]
FAME3
(#613608)		MARCHF6ADTTTCA
within TTTTA repeat region		Intron 1700–1035chr51035633910356411Familial adult myoclonic epilepsy 3[40]
FAME6
(#618074)		TNRC6AADTTTCA
within TTTTA repeat region		Intron 1?
(only 1 family)		chr162461343924613532Familial adult myoclonic epilepsy 6[68]
FAME7
(#618075)		RAPGEF2ADTTTCA
within TTTTA repeat region		Intron 14?
(only 1 family)		chr4159342527159342618Familial adult myoclonic epilepsy 7[68]
FRAXE
(#309548)		FMR2 (AFF2)XLRCCG5’ Region > 200chrX148500605148500753Mental retardation, X-linked, FRAXE type[53]
FRDA
(#229300)		FXNARGAAIntron 166–1300chr96903727569037314Friedreich ataxia[5, 19, 162]
FXS
(#300624)
FXTAS
(#300623)		FMR1XLCGG5’ Region200–3000
55–200		chrX147911979147912111Fragile X syndrome
Fragile X tremor/ataxia syndrome, premature ovarian failure 1		[162]
[56]
HD
(#143100)		HTTADCAG
(Interruptions: CAA)		Exon 136–250chr430748763074941Huntington disease[96, 101]
HDL1
(#603218)		PRNPAD24-base
octapeptide PHGGGWGQ		Exon 28–14chr2046993794699380Huntington disease-like 1[108]
HDL2
(#606438)		JPH3ADCTGExon 2A40–59chr168760428387604329Huntington disease-like 2[62]
HMNVWA1ARGGCGCGGAGCExon 13chr114357991435820Hereditary axonal motor neuropathy[121]
NIID
(#603472)		NOTCH2NLCADCGG5′ Region66–517chr1149390803149390842Neuronal intranuclear inclusion disease[55, 118, 146]
OPDM1
(#164310)		LRP12ADCGG5′ Region90–130chr8104588965104588999Oculopharyngodistal myopathy[69]
OPDM2
(#618940)		GIPC1ADCGG5’ Region70–164chr191449602914496104Oculopharyngodistal myopathy[172]
OPMD
(#164300)		PABPN1ADGCGExon 17–18chr142332147223321511Oculopharyngeal muscular dystrophy[15, 129]
OPML1
(#618637)		NUTM2B-AS1ADCGG5′ Region16–160chr107982636479826403Oculopharyngeal myopathy with leukoencephalopathy 1[69]
SBMA
(#313200)		ARXLRCAGExon 138–68chrX6754531767545419Spinal and bulbar muscular atrophy of Kennedy (Kennedy’s disease)[44, 82, 147]
SCA1
(#164400)		ATXN1ADCAG
(Interruptions: CAT)		Exon 839–91chr61632763616327723Spinocerebellar ataxia 1[120, 141]
SCA2
(#183090)		ATXN2ADCAG
(Interruptions: CAA, CGG, CGC)		Exon 133–200
(29–32
increased ALS risk)		chr12111598950111599019Spinocerebellar ataxia 2[18, 133, 141, 148]
SCA3
(#109150)		ATXN3ADCAGExon 1053–87chr149207101192071052Spinocerebellar ataxia 3[74]
SCA6
(183086)		CACNA1AADCAGExon 4719–33chr191320785813207897Spinocerebellar ataxia 6[141, 181]
SCA7
(#164500)		ATXN7ADCAGExon 134–460chr36391268563912716Spinocerebellar ataxia 7[18, 30]
SCA8
(#608768)		ATXN8ADCAG/TAG3’ UTR74–1300chr137013938370139428Spinocerebellar ataxia 8[79, 141, 155]
SCA10
(#603516)		ATXN10ADATTCT
(Interruptions: ATCCT)		Intron 9280–4500chr224579535545795424Spinocerebellar ataxia 10[88, 100, 141]
SCA12
(#604326)		PPP2R2BADCAG5’ Region51–78chr5146878729146878758Spinocerebellar ataxia 12[63, 94, 141]
SCA17
(#607136)		TBPADCAG
(Interruptions: CAT, CAA)		Exon 343–66chr6170561907170562017Spinocerebellar ataxia 17, Huntington disease-like 4[97, 115, 141]
SCA31
(#117210)		BEAN1ADTGGAA
within TAAAA and TAGAA repeat region		Intron/
Intergenic region		500–760
(> 110 TGGAA repeats)		chr166649547566495509Spinocerebellar ataxia 31[134]
SCA36
(#614153)		NOP56ADGGCCTGIntron 1650–2500chr2026527332652775Spinocerebellar ataxia 36[77]
SCA37
(#615945)		DAB1ADATTTC
within (ATTTT)7–400 repeat region		5’ Region31–75chr15736704457367125Spinocerebellar ataxia 37[139]
ULD
(#254800)		CSTBARCCCCGCCCCGCGUpstream
5’ UTR		30–125chr214377644443776479Progressive myoclonic epilepsy 1A (Unverricht and Lundborg disease)[87, 91]
ALS, amyotrophic lateral sclerosis; AS, antisense RNA; CANVAS, cerebellar ataxia neuropathy and vestibular areflexia syndrome; DM1; myotonic dystrophy 1; DM2; myotonic dystrophy 2; DRPLA, dentatorubral-pallidoluysian atrophy; EIEE1, early infantile epileptic encephalopathy 1; FAME, familial adult myoclonic epilepsy; FRAXE, fragile-XE syndrome; FRDA, Friedreich’s ataxia; FTD, frontotemporal dementia; FXS, fragile-X syndrome; FXTAS, fragile-x tremor/ataxia syndrome; HMN, hereditary motor neuropathy; HD, Huntington’s disease; HDL2, Huntington disease-like 2; HDL1, Huntington disease-like 1; LMN, lower motor neuron; NIID, neuronal intranuclear inclusion disease; OPDM, oculopharyngodistal myopathy; OPMD, oculopharyngeal muscular dystrophy; OPML, oculopharyngeal myopathy with leukoencephalopathy; SBMA, spinal and bulbar muscular atrophy; SCA, spinocerebellar ataxia; ULD, Unverricht-Lundborg disease; UMN, upper motor neuron; XLID, x-linked intellectual disability;
aThese ranges vary between studies and often the upper limit is unknown. It is important to note that these are only potentially pathogenic. There is a small (< 1%) subsection of the healthy control population who have expanded alleles with no clinical manifestations. Similarly, there are alleles lower than the given range who may have intermediate alleles and premutation syndromes
Congenital and developmental diseases caused by STR.
Phenotype (OMIM #)GeneMotifPathogenic repeat numberLocation(hg38)References
BPES
(#110100)		FOXL2GCG22–24Exonchr3138946022138946062[116]
CCHS
(#209880)		PHOX2BGCG24–33Exonchr44174597641746022[7]
DBQD2
(#615777)		XYLT1GGC100–8005’ Regionchr161747086917470967[86]
FECD3
(#613267)		TCF4TGC > 50Intronchr18a55222184a55635956a[167]
GDPAG
(#618412)		GLSGCA > 3005’ Regionchr2190880873190880920[159]
HFG
(#140000)		HOXA13GCG24–26Exonchr72719982727199967[50]
HPE5
(#609637)		ZIC2GCG25Exonchr139998544999985494[17]
HSAN8
(#616488)		PRDM12GCG18–19Exonchr9130681606130681641[23]
SPD1
(#186000)		HOXD13GCG22–29Exonchr2176093058176093099[2]
XLMR
(#300123)		SOX3GCG15–26Exonchr3181712415181712456[89]
BPES, blepharophimosis, epicanthus inversus, and ptosis; CCHS, congenital central hypoventilation syndrome; DBQD2, Desbuquois dysplasia 2; FECD3, Fuchs endothelial corneal dystrophy 3; GDPAG, global developmental delay, progressive ataxia, and elevated glutamine; HFG, hand-foot-genital syndrome; HPE5, holoprosencephaly 5; SPD1, synpolydactyly 1; XLMR, x-linked mental retardation
aLocation of entire gene listed

4. VNTR (wide sense) block

Classic minisatellites

  • Copy number variation without abrupt pathogenic threshold
  • They modulate polygenic risk (INS → type 1 diabetes) or cause structural disease (MUC1 → ADTKD)
  • Historical basis of forensic DNA fingerprinting

Macrosatellites

— FSHD as a paradigmatic case

  • D4Z4 (subtelomere 4q35): 3.3 kb unit
  • Normal: 11-100 copies / Pathological: ≤10 copies (FSHD1) — contraction, not expansion
  • Contraction opens chromatin → derepression of DUX4 (normally silenced in adult muscle) → toxicity
  • Requires permissive 4qA haplotype (same contraction in 4qB does not cause disease)
  • FSHD2: normal array, but mutation in SMCHD1 → same result (DUX4 derepression) via trans route, not via cis contraction
  • Does not follow classical genetic anticipation (epigenetic mechanism, not repetition race)
  • Yes, there is a small but important group of diseases that share with FSHD the “atypical” mechanism (large repeat, classic non-microsatellite, and/or epigenetic mechanism instead of direct toxicity). The most relevant ones for your scheme:

—- ICF Syndrome (Immunodeficiency, Centromeric Instability, Facial Anomalies)

  • Affects satellite repeats 2 and 3 (pericentromeric sequences, not D4Z4, but same principle of macrosatellite/repetitive heterochromatin)
  • Mechanism: mutations in DNMT3B (o ZBTB24, CDCA7, HELLS) → hypomethylation of these repeated regions → pericentromeric decondensation → chromosomal instability
  • It is practically the autosomal recessive equivalent of the FSHD2 mechanism: the machinery that keeps the repetitive heterochromatin silenced fails, rather than the repetition itself.

—- Progressive myoclonic epilepsy type 1 (Unverricht-Lundborg).

  • gene CSTB (cystatin B)
  • Repetition dodecamera (12 bp) in the promoter — border size between microsatellite and minisatellite, another case that does not fit cleanly in classical STR
  • Mechanism: expansion (unlike FSHD) but the result is loss of function due to transcriptional reduction, not protein or RNA toxicity — expansion in the promoter simply makes it difficult to transcribe the gene
  • Useful as contrast: expansion causing pure loss of function, no toxic gain
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