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NM_032578.4(MYPN):c.3127del (p.Ser1043fs) AND Dilated cardiomyopathy 1KK

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 8, 2024
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000818659.5

Allele description [Variation Report for NM_032578.4(MYPN):c.3127del (p.Ser1043fs)]

NM_032578.4(MYPN):c.3127del (p.Ser1043fs)

Gene:
MYPN:myopalladin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q21.3
Genomic location:
Preferred name:
NM_032578.4(MYPN):c.3127del (p.Ser1043fs)
HGVS:
  • NC_000010.11:g.68195501del
  • NG_032118.1:g.94385del
  • NM_001256267.2:c.3127del
  • NM_001256268.2:c.2245del
  • NM_032578.4:c.3127delMANE SELECT
  • NP_001243196.1:p.Ser1043fs
  • NP_001243197.1:p.Ser749fs
  • NP_115967.2:p.Ser1043fs
  • LRG_410:g.94385del
  • NC_000010.10:g.69955258del
  • NM_032578.3:c.3127delA
  • NR_045662.4:n.2664del
  • NR_045663.4:n.3201del
Protein change:
S1043fs
Links:
dbSNP: rs1589608098
NCBI 1000 Genomes Browser:
rs1589608098
Molecular consequence:
  • NM_001256267.2:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001256268.2:c.2245del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_032578.4:c.3127del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NR_045662.4:n.2664del - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_045663.4:n.3201del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Dilated cardiomyopathy 1KK (CMD1KK)
Identifiers:
MONDO: MONDO:0014100; MedGen: C3714995; Orphanet: 154; Orphanet: 75249; OMIM: 615248

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    Assertion and evidence details

    Help
    Submission AccessionSubmitterReview Status
    (Assertion method)    		Clinical Significance
    (Last evaluated)    		OriginMethodCitations
    SCV000959284Labcorp Genetics (formerly Invitae), Labcorp
    criteria provided, single submitter

    (Invitae Variant Classification Sherloc (09022015))    		Pathogenic
    (Jan 8, 2024)     		germlineclinical testing

    PubMed (2)
    [See all records that cite these PMIDs]

    Help

    Summary from all submissions

    EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
    not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

    Citations

    PubMed

    Biallelic Mutations in MYPN, Encoding Myopalladin, Are Associated with Childhood-Onset, Slowly Progressive Nemaline Myopathy.

    Miyatake S, Mitsuhashi S, Hayashi YK, Purevjav E, Nishikawa A, Koshimizu E, Suzuki M, Yatabe K, Tanaka Y, Ogata K, Kuru S, Shiina M, Tsurusaki Y, Nakashima M, Mizuguchi T, Miyake N, Saitsu H, Ogata K, Kawai M, Towbin J, Nonaka I, Nishino I, et al.

    Am J Hum Genet. 2017 Jan 5;100(1):169-178. doi: 10.1016/j.ajhg.2016.11.017. Epub 2016 Dec 22.

    PubMed [citation]
    PMID:
    28017374
    PMCID:
    PMC5223057

    Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

    Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

    Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

    PubMed [citation]
    PMID:
    28492532
    PMCID:
    PMC5632818

    Details of each submission

    From Labcorp Genetics (formerly Invitae), Labcorp, SCV000959284.4

    #EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
    1not providednot providednot providednot providedclinical testing PubMed (2)

    Description

    This sequence change creates a premature translational stop signal (p.Ser1043Valfs*3) in the MYPN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MYPN are known to be pathogenic (PMID: 28017374). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with MYPN-related conditions. ClinVar contains an entry for this variant (Variation ID: 661274). For these reasons, this variant has been classified as Pathogenic.

    #SampleMethodObservation
    OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
    1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

    Last Updated: Sep 29, 2024