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NM_000337.6(SGCD):c.593G>A (p.Arg198Gln) AND Autosomal recessive limb-girdle muscular dystrophy type 2F

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Feb 8, 2023
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:
RCV000706996.6

Allele description

NM_000337.6(SGCD):c.593G>A (p.Arg198Gln)

Gene:
SGCD:sarcoglycan delta [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
5q33.3
Genomic location:
Preferred name:
NM_000337.6(SGCD):c.593G>A (p.Arg198Gln)
HGVS:
  • NC_000005.10:g.156757598G>A
  • NG_008693.2:g.892256G>A
  • NM_000337.6:c.593G>AMANE SELECT
  • NM_001128209.2:c.590G>A
  • NM_172244.3:c.593G>A
  • NP_000328.2:p.Arg198Gln
  • NP_000328.2:p.Arg198Gln
  • NP_001121681.1:p.Arg197Gln
  • NP_758447.1:p.Arg198Gln
  • LRG_205t1:c.593G>A
  • LRG_205:g.892256G>A
  • LRG_205p1:p.Arg198Gln
  • NC_000005.9:g.156184609G>A
  • NM_000337.5:c.593G>A
Protein change:
R197Q
Links:
dbSNP: rs750459196
NCBI 1000 Genomes Browser:
rs750459196
Molecular consequence:
  • NM_000337.6:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001128209.2:c.590G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172244.3:c.593G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive limb-girdle muscular dystrophy type 2F (LGMDR6)
Synonyms:
Limb-girdle muscular dystrophy, type 2F; Muscular dystrophy limb-girdle with delta-sarcoglyan deficiency; MUSCULAR DYSTROPHY, LIMB-GIRDLE, AUTOSOMAL RECESSIVE 6
Identifiers:
MONDO: MONDO:0011028; MedGen: C1832525; Orphanet: 219; OMIM: 601287

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000836072Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Sep 1, 2022)
germlineclinical testing

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

SCV003931881Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Feb 8, 2023)
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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Invitae, SCV000836072.3

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 198 of the SGCD protein (p.Arg198Gln). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with SGCD-related conditions. ClinVar contains an entry for this variant (Variation ID: 582822). 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: "Deleterious"; PolyPhen-2: "Probably 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.

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

From Genome-Nilou Lab, SCV003931881.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 11, 2024