NM_000337.6(SGCD):c.32G>A (p.Arg11Gln) AND Autosomal recessive limb-girdle muscular dystrophy type 2F

Germline classification:: Uncertain significance (3 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:: RCV001043670.7

Allele description [Variation Report for NM_000337.6(SGCD):c.32G>A (p.Arg11Gln)]

NM_000337.6(SGCD):c.32G>A (p.Arg11Gln)

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.32G>A (p.Arg11Gln)

Other names:

p.R11Q:CGG>CAG; NM_001128209.1:c.29G>A; NM_172244.2:c.32G>A; XM_005265965.1:c.32G>A; XM_005265966.1:c.32G>A; XM_005265967.1:c.32G>A

HGVS:

NC_000005.10:g.156344517G>A
NG_008693.2:g.479174G>A
NM_000337.6:c.32G>AMANE SELECT
NM_001128209.2:c.29G>A
NM_172244.3:c.32G>A
NP_000328.2:p.Arg11Gln
NP_000328.2:p.Arg11Gln
NP_001121681.1:p.Arg10Gln
NP_758447.1:p.Arg11Gln
LRG_205t1:c.32G>A
LRG_205:g.479174G>A
LRG_205p1:p.Arg11Gln
NC_000005.9:g.155771527G>A
NM_000337.5:c.32G>A

Protein change:

R10Q

Links:

dbSNP: rs752548592

NCBI 1000 Genomes Browser:

rs752548592

Molecular consequence:

NM_000337.6:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128209.2:c.29G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_172244.3:c.32G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001207428	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 3, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002099069	New York Genome Center - CSER-NYCKidSeq	criteria provided, single submitter (NYGC Assertion Criteria 2020)	Uncertain significance (Apr 10, 2021)	inherited	clinical testing	Citation Link,
SCV003931767	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Feb 8, 2023)	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

SCV001207428

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 3, 2022)

germline

clinical testing

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

SCV002099069

New York Genome Center - CSER-NYCKidSeq

criteria provided, single submitter

(NYGC Assertion Criteria 2020)

Uncertain significance
(Apr 10, 2021)

inherited

clinical testing

Citation Link,

SCV003931767

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Feb 8, 2023)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	inherited	unknown	1	not provided	not provided	1	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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001207428.4

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

Description

This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 11 of the SGCD protein (p.Arg11Gln). This variant is present in population databases (rs752548592, gnomAD 0.02%). 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: 196256). 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.

#	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

From New York Genome Center - CSER-NYCKidSeq, SCV002099069.1

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

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

From Genome-Nilou Lab, SCV003931767.1

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

#	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: Sep 29, 2024

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