Inheritance

Autosomal dominant

Prevalence

 1-9 / 100 000

Source:ORPHA:606

Rapid or full curation?

ClinGen / GenCC / BabySeq / HGMD / OMIM

ClinGen - none. GenCC - Strong (Invitae), BabySeq - none. HGMD - 1 entry for repeat expansions.

Clinical Validity Scoring Notes and points

Liquori 2001 (PMID: 11486088) - mapped the MD2 locus and used positional cloning to identify the DM2 mutation. Per text, all 51 affected individuals in 6 DM2 families were found to have expanded alleles (confirmed by Southern and PCR, counting max 3 POINT SEGREGATION) Sequencing revealed a complex repeat motif ( TG)n( TCTG)n(CCTG)n. In controls this tract ranged from 104-176 basepairs. The largest repeat tract in normal controls had 26 CCTG repeats with two interruptions. Three families with a total of 6 individuals with expansions of the CCTG repeat (fig 1D), 3 segregations. Expanded alleles ranged from 75-1100 CCTG repeats (6 families with expansions, 1 proband each family 0.5x6 variant points, 3 VARIANT POINTS).

Bachinski 2003 (PMID: 12970845) - 17 kindreds of European origins link to the locus. Fig 2 shows a family with expansion found in RP-PCR. Counting segs based on RP-PCR results: III:2 proband, segregations in III:3, III:4, IV:2, II:1 (obligate), II:3, II:6. Total of 6 segs. Per the text, linkage was done for 17 families with DM2. The expansion was present in the kindreds as confirmed by Southern. (17x0.5 = 8.5 variant points)

Nakayama 2014 (PMID: 24430576) - family with DM2, proband found to have 3400 CCTG repeats. Repetition over time.

Wei 2018 PMID:29735719. Immunofluorescence of muscle from DM2 patients and controls found that CNBP localized in cytoplasm in control tissue whereas it localized primarily ni membrane of DM2 fibers. Animal model - CNBP knockout mouse had muscle atrophy at young age, heterozygous mice had severe muscle loss only at advanced age. Since the KO mice aren’t true replications of the expanded allele, not scoring. Functional alteration in patient cells - 1 POINT EXPERIMENTAL

Raheem 2010 PMID: 20971734 - In differentiating myoblasts, in patients with DM2, ZNF9 was abnormally expressed. There was overall reduction in mRNA and protein levels. The subcellular localization was more membrane bound. Splice variant analysis indicated retention of intron 3. Functional alteration in non-patient cells 0.5 points experimental.

12 points genetic (max allowed) + 1.5 points experimental

Clinical Validity Points Total

13.5 points

Clinical Validity Classification

Definitive

Source: 11486088, 12970845, 29735719, 20971734

Molecular Mechanism

Short tandem repeats ONLY (no other variant type reported)

STR expansion - complex motif (TG)_n(TCTG)_n(CCTG)_n . Other labs report by the basepair size; however, we will get CCTG repeat size. It is the expansion of this tract that has been associated with disease.

• Normal: 27

• Pathogenic >75

• Premutation: 30-54

• Uncertain significance - large range (see GeneReviews)

• Cutoff: 27

  • Note gnomad has >100 alleles over this size, would contribute to # needing review for us

Literature:

• GeneReviews PMID: 20301639 - normal ≤30 uninterrupted CCTG repeats OR 11-26 CCTG repeats with any GCTC or TCTG interruptions. Unknown significance (normal vs. mutable) 27-29 CCTG repeats. Mutable normal (premutatio) ~30-~54 CCTG repeats. Unknown significance (premutation vs pathogenic) ~55-74 ~55-74 CCTG repeats. Pathogenic ~75-11,000 CCTG repeats.

  • “Due to variability in the TG and TCTG portions of the repeat tract, a total repeat size in base pairs is frequently reported and CCTG repeat length is often estimated [Liquori et al 2001, Liquori et al 2003, Radvanszky et al 2013, Mahyera et al 2018].”

• gnomAD Normal ≤ 54, Pathogenic ≥ 55

• Stripy - normal ≤29, intermediate 30-55, pathogenic ≥55

• Not in the Mayo paper https://docs.google.com/spreadsheets/d/189Ph82ZPDhHwgTtmmPpCItan8boniGIL/edit#gid=1020718149

• Other labs:

  • labcorp - pathogenic is over 75. Athena - Normal: Less than 177 base pairs. Mayo (sends to Athena). Sample report shows Normal (<177 base pairs), Borderline (177-372 base pairs), Positive (>372 base pairs) Fulgent, not provided. GeneDx - Normal alleles have 26 or less CCTG repeats and disease alleles have 75 or more repeats. Disease alleles can contain more than 11,000 repeats, with an average of 5,000 repeats.1

• Liquori 2001 (PMID: 11486088) - largest normal was 26 CCTG repeats, smallest pathogenic reported to be 75 CCTG repeats.

• Sukel 2018 29588063 - Polish controls had 110-228bp alleles. For confirmed probands. Majority of control alleles were 110-158bp. The presence of expanded alleles in the CNBP gene was found in 188 of the subjects from 122 families.

• Mahyera 2018 29973908 - Two premutation families studied, results support that premutation range of unstable CCTG stretches lie between 25-75 repeats.

• Botta 2021 PMID: 34234810 - Italian cohort. DM2 molecular diagnosis confirmed in 187/570 samples analyzed with 25 different alleles ranging from 108 to 168bp. They identified the presence of an uninterrupted CCTG tract below 26 repetitions which is considered The general structure of the normal repeat motif is (TG)14−26(TCTG)7−11(CCTG)5−9(NCTG)3−5(CCTG)4−8. Fig 5 shows premutations, all range from 37 to 55, though these individuals do appear to have some clinical features.

• INTERRUPTIONS:

  • Large uninterrupted repeat lengths have decreased stability.

Penetrance

(list source/PMID)

Moderate / Low

Source: 11486088

Age of Onset

(list source/PMID)

Adulthood, late adulthood

Severity

Moderate

Clinical Features

myotonia and muscle dysfunction (proximal and axial weakness, myalgia, and stiffness)

cataracts

cardiac conduction defects

insulin-insensitive type 2 diabetes mellitus

Sources: PMID: 20301639

HPO Terms

https://hpo.jax.org/app/

Gene SOPs & Notes

short tandem repeat expansions are the only known variant associated with disease, see mol. mech section

Curation Summary

The CNBP gene is associated with autosomal dominant myotonic dystrophy type 2, which is characterized by myotonia and muscle dysfunction, cataracts, cardiac conduction defects, and type 2 diabetes. It is caused by a short tandem repeat expansion. Age of onset is in adulthood, severity can vary, and reduced penetrance has been observed (PMID: 20301639, 11486088)

Case ID, Curator name, Date, Jira ticket link

Andrea Oza 09.29.2023 https://broadinstitute.atlassian.net/browse/BCL-168