rs1555326546

Variant names:

• chr14-50911725-AGTAC-A
• rs1555326546
• NM_002863.5:c.1969+1_1969+4delGTAC

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1 PM2

The NM_002863.5(PYGL):​c.1969+1_1969+4delGTAC variant causes a splice donor, splice region, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as no classification for the single variant (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PYGL NM_002863.5 splice_donor, splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 9.29

Genes affected

PYGL (HGNC:9725): (glycogen phosphorylase L) This gene encodes a homodimeric protein that catalyses the cleavage of alpha-1,4-glucosidic bonds to release glucose-1-phosphate from liver glycogen stores. This protein switches from inactive phosphorylase B to active phosphorylase A by phosphorylation of serine residue 15. Activity of this enzyme is further regulated by multiple allosteric effectors and hormonal controls. Humans have three glycogen phosphorylase genes that encode distinct isozymes that are primarily expressed in liver, brain and muscle, respectively. The liver isozyme serves the glycemic demands of the body in general while the brain and muscle isozymes supply just those tissues. In glycogen storage disease type VI, also known as Hers disease, mutations in liver glycogen phosphorylase inhibit the conversion of glycogen to glucose and results in moderate hypoglycemia, mild ketosis, growth retardation and hepatomegaly. Alternative splicing results in multiple transcript variants encoding different isoforms.[provided by RefSeq, Feb 2011]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, LoF is a know mechanism of disease, No cryptic splice site detected. Exon removal results in frameshift change.
• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYGL	NM_002863.5	c.1969+1_1969+4delGTAC		splice_donor_variant, splice_region_variant, intron_variant	Intron 16 of 19	ENST00000216392.8	NP_002854.3
PYGL	NM_001163940.2	c.1867+1_1867+4delGTAC		splice_donor_variant, splice_region_variant, intron_variant	Intron 15 of 18		NP_001157412.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PYGL	ENST00000216392.8	c.1969+1_1969+4delGTAC		splice_donor_variant, splice_region_variant, intron_variant	Intron 16 of 19	1	NM_002863.5	ENSP00000216392.7
PYGL	ENST00000532462.5	c.1969+1_1969+4delGTAC		splice_donor_variant, splice_region_variant, intron_variant	Intron 16 of 19	1		ENSP00000431657.1
PYGL	ENST00000544180.6	c.1867+1_1867+4delGTAC		splice_donor_variant, splice_region_variant, intron_variant	Intron 15 of 18	2		ENSP00000443787.1
PYGL	ENST00000532107.2	n.142+1_142+4delGTAC		splice_donor_variant, splice_region_variant, intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DL_spliceai		1.0		Position offset: 5

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1555326546; hg19: chr14-51378443;