chr12-21536386-AT-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_021957.4(GYS2):c.*567del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000328 in 152,250 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000033 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GYS2
NM_021957.4 3_prime_UTR
NM_021957.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.479
Genes affected
GYS2 (HGNC:4707): (glycogen synthase 2) The protein encoded by this gene, liver glycogen synthase, catalyzes the rate-limiting step in the synthesis of glycogen - the transfer of a glucose molecule from UDP-glucose to a terminal branch of the glycogen molecule. Mutations in this gene cause glycogen storage disease type 0 (GSD-0) - a rare type of early childhood fasting hypoglycemia with decreased liver glycogen content. [provided by RefSeq, Dec 2009]
SPX (HGNC:28139): (spexin hormone) The protein encoded by this gene is a hormone involved in modulation of cardiovascular and renal function. It has also been shown in rats to cause weight loss. Several transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GYS2 | NM_021957.4 | c.*567del | 3_prime_UTR_variant | 16/16 | ENST00000261195.3 | ||
LOC124902896 | XR_007063240.1 | n.519-658del | intron_variant, non_coding_transcript_variant | ||||
GYS2 | XM_006719063.4 | c.*567del | 3_prime_UTR_variant | 15/15 | |||
GYS2 | XM_024448960.2 | c.*42+525del | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GYS2 | ENST00000261195.3 | c.*567del | 3_prime_UTR_variant | 16/16 | 1 | NM_021957.4 | P1 | ||
SPX | ENST00000537527.1 | n.472-658del | intron_variant, non_coding_transcript_variant | 3 | |||||
SPX | ENST00000649016.1 | n.529-658del | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152250Hom.: 1 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 4606Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 2472
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152250Hom.: 1 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74376
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glycogen storage disorder due to hepatic glycogen synthase deficiency Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at