NM_001353214.3(DYM):c.1849G>A (p.Asp617Asn) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 30, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV001769422.6

Allele description [Variation Report for NM_001353214.3(DYM):c.1849G>A (p.Asp617Asn)]

NM_001353214.3(DYM):c.1849G>A (p.Asp617Asn)

Gene:

DYM:dymeclin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.1

Genomic location:

Preferred name:

NM_001353214.3(DYM):c.1849G>A (p.Asp617Asn)

HGVS:

NC_000018.10:g.49118806C>T
NG_009239.2:g.346928G>A
NM_001353210.3:c.1681G>A
NM_001353211.3:c.1681G>A
NM_001353212.3:c.1846G>A
NM_001353213.3:c.1846G>A
NM_001353214.3:c.1849G>AMANE SELECT
NM_001353215.3:c.1729-21291G>A
NM_001353216.3:c.1564-21291G>A
NM_001374428.1:c.1849G>A
NM_001374429.1:c.1843G>A
NM_001374430.1:c.1849G>A
NM_001374431.1:c.1849G>A
NM_001374432.1:c.1723G>A
NM_001374433.1:c.1684G>A
NM_001374434.1:c.1684G>A
NM_001374435.1:c.1681G>A
NM_001374436.1:c.1558G>A
NM_001374437.1:c.1501G>A
NM_001374438.1:c.1561-21291G>A
NM_001374439.1:c.1558-21291G>A
NM_001374440.1:c.1456G>A
NM_001374441.1:c.1279G>A
NM_001374442.1:c.1114G>A
NM_001374443.1:c.1111G>A
NM_001374444.1:c.994-21291G>A
NM_017653.6:c.1684G>A
NP_001340139.1:p.Asp561Asn
NP_001340140.1:p.Asp561Asn
NP_001340141.1:p.Asp616Asn
NP_001340142.1:p.Asp616Asn
NP_001340143.1:p.Asp617Asn
NP_001361357.1:p.Asp617Asn
NP_001361358.1:p.Asp615Asn
NP_001361359.1:p.Asp617Asn
NP_001361360.1:p.Asp617Asn
NP_001361361.1:p.Asp575Asn
NP_001361362.1:p.Asp562Asn
NP_001361363.1:p.Asp562Asn
NP_001361364.1:p.Asp561Asn
NP_001361365.1:p.Asp520Asn
NP_001361366.1:p.Asp501Asn
NP_001361369.1:p.Asp486Asn
NP_001361370.1:p.Asp427Asn
NP_001361371.1:p.Asp372Asn
NP_001361372.1:p.Asp371Asn
NP_060123.3:p.Asp562Asn
NC_000018.9:g.46645176C>T
NM_017653.3:c.1684G>A

Protein change:

D371N

Links:

dbSNP: rs769667648

NCBI 1000 Genomes Browser:

rs769667648

Molecular consequence:

NM_001353215.3:c.1729-21291G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001353216.3:c.1564-21291G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374438.1:c.1561-21291G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374439.1:c.1558-21291G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001374444.1:c.994-21291G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001353210.3:c.1681G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353211.3:c.1681G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353212.3:c.1846G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353213.3:c.1846G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001353214.3:c.1849G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374428.1:c.1849G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374429.1:c.1843G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374430.1:c.1849G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374431.1:c.1849G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374432.1:c.1723G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374433.1:c.1684G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374434.1:c.1684G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374435.1:c.1681G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374436.1:c.1558G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374437.1:c.1501G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374440.1:c.1456G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374441.1:c.1279G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374442.1:c.1114G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001374443.1:c.1111G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_017653.6:c.1684G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002001305	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 30, 2024)	germline	clinical testing	Citation Link,
SCV003028198	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 12, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002001305

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Aug 30, 2024)

germline

clinical testing

Citation Link,

SCV003028198

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 12, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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 GeneDx, SCV002001305.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003028198.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This variant has not been reported in the literature in individuals affected with DYM-related conditions. ClinVar contains an entry for this variant (Variation ID: 1313776). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant is present in population databases (rs769667648, gnomAD 0.006%). This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 562 of the DYM protein (p.Asp562Asn).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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