VCV000471335.7 - ClinVar

NM_000023.4(SGCA):c.588_599del (p.Tyr197_Val200del)

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Uncertain significance

This classification is based on the single submission received

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000023.4(SGCA):c.588_599del (p.Tyr197_Val200del)

Variation ID: 471335 Accession: VCV000471335.7

Type and length

Deletion, 12 bp

Location

Cytogenetic: 17q21.33 17: 50169092-50169103 (GRCh38) [ NCBI UCSC ] 17: 48246453-48246464 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Dec 26, 2017	Feb 15, 2026	Oct 1, 2016

HGVS

Nucleotide	Protein	Molecular consequence
NM_000023.4:c.588_599del MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000014.1:p.Tyr197_Val200del	inframe deletion
NM_001135697.3:c.584+523_584+534del		intron variant
NR_135553.2:n.624_635del		non-coding transcript variant
NC_000017.11:g.50169095_50169106del
NC_000017.10:g.48246456_48246467del
NG_008889.1:g.8091_8102del
LRG_203:g.8091_8102del
LRG_203t1:c.588_599del

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000017.11:50169091:GGTATACATTAAGGT:GGT

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA658656730 dbSNP: rs1555568966 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
SGCA		-	-	GRCh38 GRCh37	836	861

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Autosomal recessive limb-girdle muscular dystrophy type 2D	Uncertain significance (1)	criteria provided, single submitter	Oct 1, 2016	RCV000549897.7

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Uncertain significance (Oct 01, 2016) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Autosomal recessive limb-girdle muscular dystrophy type 2D	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000649776.6 First in ClinVar: Dec 26, 2017 Last updated: Feb 15, 2026	Comment: show In summary, this variant is a novel in-frame deletion with uncertain impact on protein function. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SGCA-related disease. This sequence change deletes 12 nucleotides from exon 6 of the SGCA mRNA (c.588_599delATACATTAAGGT). This leads to the deletion of 4 amino acid residues in the SGCA protein (p.Tyr197_Val200del) but otherwise preserves the integrity of the reading frame. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Comment:

In summary, this variant is a novel in-frame deletion with uncertain impact on protein function. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may alter RNA splicing, but this prediction has not been confirmed by published transcriptional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a SGCA-related disease. This sequence change deletes 12 nucleotides from exon 6 of the SGCA mRNA (c.588_599delATACATTAAGGT). This leads to the deletion of 4 amino acid residues in the SGCA protein (p.Tyr197_Val200del) but otherwise preserves the integrity of the reading frame.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1555568966 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Feb 15, 2026