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NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Sep 15, 2022
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:
RCV001851607.6

Allele description [Variation Report for NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter)]

NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter)

Gene:
DYM:dymeclin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
18q21.1
Genomic location:
Preferred name:
NM_001353214.3(DYM):c.396T>A (p.Tyr132Ter)
HGVS:
  • NC_000018.10:g.49378592A>T
  • NG_009239.2:g.87142T>A
  • NM_001353210.3:c.396T>A
  • NM_001353211.3:c.393T>A
  • NM_001353212.3:c.393T>A
  • NM_001353213.3:c.396T>A
  • NM_001353214.3:c.396T>AMANE SELECT
  • NM_001353215.3:c.396T>A
  • NM_001353216.3:c.396T>A
  • NM_001374428.1:c.396T>A
  • NM_001374429.1:c.393T>A
  • NM_001374430.1:c.396T>A
  • NM_001374431.1:c.396T>A
  • NM_001374432.1:c.396T>A
  • NM_001374433.1:c.396T>A
  • NM_001374434.1:c.396T>A
  • NM_001374435.1:c.396T>A
  • NM_001374436.1:c.396T>A
  • NM_001374437.1:c.396T>A
  • NM_001374438.1:c.396T>A
  • NM_001374439.1:c.393T>A
  • NM_001374440.1:c.193+13001T>A
  • NM_001374441.1:c.193+13001T>A
  • NM_001374442.1:c.193+13001T>A
  • NM_001374443.1:c.193+13001T>A
  • NM_001374444.1:c.193+13001T>A
  • NM_017653.6:c.396T>A
  • NP_001340139.1:p.Tyr132Ter
  • NP_001340140.1:p.Tyr131Ter
  • NP_001340141.1:p.Tyr131Ter
  • NP_001340142.1:p.Tyr132Ter
  • NP_001340143.1:p.Tyr132Ter
  • NP_001340144.1:p.Tyr132Ter
  • NP_001340145.1:p.Tyr132Ter
  • NP_001361357.1:p.Tyr132Ter
  • NP_001361358.1:p.Tyr131Ter
  • NP_001361359.1:p.Tyr132Ter
  • NP_001361360.1:p.Tyr132Ter
  • NP_001361361.1:p.Tyr132Ter
  • NP_001361362.1:p.Tyr132Ter
  • NP_001361363.1:p.Tyr132Ter
  • NP_001361364.1:p.Tyr132Ter
  • NP_001361365.1:p.Tyr132Ter
  • NP_001361366.1:p.Tyr132Ter
  • NP_001361367.1:p.Tyr132Ter
  • NP_001361368.1:p.Tyr131Ter
  • NP_060123.3:p.Tyr132Ter
  • NC_000018.9:g.46904962A>T
  • NM_017653.3:c.396T>A
  • NM_017653.5:c.396T>A
Protein change:
Y131*; TYR132TER
Links:
OMIM: 607461.0003; dbSNP: rs120074162
NCBI 1000 Genomes Browser:
rs120074162
Molecular consequence:
  • NM_001374440.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374441.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374442.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374443.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001374444.1:c.193+13001T>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001353210.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353211.3:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353212.3:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353213.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353214.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353215.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001353216.3:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374428.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374429.1:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374430.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374431.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374432.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374433.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374434.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374435.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374436.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374437.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374438.1:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001374439.1:c.393T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_017653.6:c.396T>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002152740Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Sep 15, 2022) 		germlineclinical testing

PubMed (4)
[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

Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene.

Cohn DH, Ehtesham N, Krakow D, Unger S, Shanske A, Reinker K, Powell BR, Rimoin DL.

Am J Hum Genet. 2003 Feb;72(2):419-28. Epub 2002 Dec 16.

PubMed [citation]
PMID:
12491225
PMCID:
PMC420018

Mutations in a novel gene Dymeclin (FLJ20071) are responsible for Dyggve-Melchior-Clausen syndrome.

El Ghouzzi V, Dagoneau N, Kinning E, Thauvin-Robinet C, Chemaitilly W, Prost-Squarcioni C, Al-Gazali LI, Verloes A, Le Merrer M, Munnich A, Trembath RC, Cormier-Daire V.

Hum Mol Genet. 2003 Feb 1;12(3):357-64.

PubMed [citation]
PMID:
12554689
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002152740.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 3186). This premature translational stop signal has been observed in individual(s) with Dyggve-Melchior-Clausen syndrome (PMID: 12491225). This variant is present in population databases (rs120074162, gnomAD 0.007%). This sequence change creates a premature translational stop signal (p.Tyr132*) in the DYM gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DYM are known to be pathogenic (PMID: 12491225, 12554689, 18996921).

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

Last Updated: Sep 29, 2024