NM_000337.6(SGCD):c.494G>A (p.Arg165Gln) 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:: RCV000700991.8

Allele description [Variation Report for NM_000337.6(SGCD):c.494G>A (p.Arg165Gln)]

NM_000337.6(SGCD):c.494G>A (p.Arg165Gln)

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.494G>A (p.Arg165Gln)

HGVS:

NC_000005.10:g.156595043G>A
NG_008693.2:g.729700G>A
NM_000337.6:c.494G>AMANE SELECT
NM_001128209.2:c.491G>A
NM_172244.3:c.494G>A
NP_000328.2:p.Arg165Gln
NP_000328.2:p.Arg165Gln
NP_001121681.1:p.Arg164Gln
NP_758447.1:p.Arg165Gln
LRG_205t1:c.494G>A
LRG_205:g.729700G>A
LRG_205p1:p.Arg165Gln
NC_000005.9:g.156022053G>A
NM_000337.5:c.494G>A
NM_172244.2:c.494G>A

Protein change:

R164Q

Links:

dbSNP: rs727503423

NCBI 1000 Genomes Browser:

rs727503423

Molecular consequence:

NM_000337.6:c.494G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001128209.2:c.491G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_172244.3:c.494G>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000829771	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 13, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003931859	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

SCV000829771

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 13, 2022)

germline

clinical testing

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

SCV003931859

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

Citations

PubMed

Nothing to display

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000829771.6

#	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 165 of the SGCD protein (p.Arg165Gln). 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: 165234). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SGCD protein function. 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 Genome-Nilou Lab, SCV003931859.1

#	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: Oct 8, 2024

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