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NM_004393.6(DAG1):c.1690C>A (p.Leu564Ile) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 25, 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:
RCV000704955.4

Allele description [Variation Report for NM_004393.6(DAG1):c.1690C>A (p.Leu564Ile)]

NM_004393.6(DAG1):c.1690C>A (p.Leu564Ile)

Gene:
DAG1:dystroglycan 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p21.31
Genomic location:
Preferred name:
NM_004393.6(DAG1):c.1690C>A (p.Leu564Ile)
HGVS:
  • NC_000003.12:g.49532201C>A
  • NG_013230.4:g.67070C>A
  • NM_001165928.4:c.1690C>A
  • NM_001177634.3:c.1690C>A
  • NM_001177635.3:c.1690C>A
  • NM_001177636.3:c.1690C>A
  • NM_001177637.3:c.1690C>A
  • NM_001177638.3:c.1690C>A
  • NM_001177639.3:c.1690C>A
  • NM_001177640.3:c.1690C>A
  • NM_001177641.3:c.1690C>A
  • NM_001177642.3:c.1690C>A
  • NM_001177643.3:c.1690C>A
  • NM_001177644.3:c.1690C>A
  • NM_004393.6:c.1690C>AMANE SELECT
  • NP_001159400.3:p.Leu564Ile
  • NP_001171105.2:p.Leu564Ile
  • NP_001171106.2:p.Leu564Ile
  • NP_001171107.2:p.Leu564Ile
  • NP_001171108.2:p.Leu564Ile
  • NP_001171109.2:p.Leu564Ile
  • NP_001171110.2:p.Leu564Ile
  • NP_001171111.2:p.Leu564Ile
  • NP_001171112.2:p.Leu564Ile
  • NP_001171113.2:p.Leu564Ile
  • NP_001171114.2:p.Leu564Ile
  • NP_001171115.2:p.Leu564Ile
  • NP_004384.4:p.Leu564Ile
  • NP_004384.5:p.Leu564Ile
  • LRG_854t1:c.1690C>A
  • LRG_854t2:c.1690C>A
  • LRG_854:g.67070C>A
  • LRG_854p1:p.Leu564Ile
  • LRG_854p2:p.Leu564Ile
  • NC_000003.11:g.49569634C>A
  • NM_004393.4:c.1690C>A
  • NM_004393.5:c.1690C>A
Protein change:
L564I
Links:
dbSNP: rs199894361
NCBI 1000 Genomes Browser:
rs199894361
Molecular consequence:
  • NM_001165928.4:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177634.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177635.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177636.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177637.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177638.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177639.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177640.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177641.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177642.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177643.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001177644.3:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004393.6:c.1690C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2P
Synonyms:
MUSCULAR DYSTROPHY-DYSTROGLYCANOPATHY, LIMB-GIRDLE, DAG1-RELATED; Limb-girdle muscular dystrophy-dystroglycanopathy, type C9; MUSCULAR DYSTROPHY, LIMB-GIRDLE, TYPE 2P; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0013440; MedGen: C4511963; Orphanet: 280333; OMIM: 613818
Name:
Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9
Synonyms:
WALKER-WARBURG SYNDROME OR MUSCLE-EYE BRAIN DISEASE, DAG1-RELATED; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 9
Identifiers:
MONDO: MONDO:0014683; MedGen: C4225291; Orphanet: 370997; Orphanet: 899; OMIM: 616538

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000833930Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Jul 25, 2022)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000833930.3

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

Description

This sequence change replaces leucine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 564 of the DAG1 protein (p.Leu564Ile). This variant is present in population databases (rs199894361, gnomAD 0.2%). This variant has not been reported in the literature in individuals affected with DAG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 283248). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

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

Last Updated: Feb 4, 2024