NM_002863.5:c.664G>A

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002863.5(PYGL):c.664G>A(p.Val222Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0679 in 1,610,242 control chromosomes in the GnomAD database, including 4,607 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.095 ( 925 hom., cov: 32)

Exomes 𝑓: 0.065 ( 3682 hom. )

Consequence

PYGL
NM_002863.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 4.12

Variant links:

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]

PYGL links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017901957).

BP6

Variant 14-50921064-C-T is Benign according to our data. Variant chr14-50921064-C-T is described in ClinVar as [Benign]. Clinvar id is 258846.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PYGL	NM_002863.5 link	c.664G>A	p.Val222Ile	missense_variant	Exon 6 of 20	ENST00000216392.8	NP_002854.3	P06737-1
PYGL	NM_001163940.2 link	c.562G>A	p.Val188Ile	missense_variant	Exon 5 of 19		NP_001157412.1	P06737-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
PYGL	ENST00000216392.8 link	c.664G>A	p.Val222Ile	missense_variant	Exon 6 of 20	1	NM_002863.5	ENSP00000216392.7	P06737-1
PYGL	ENST00000532462.5 link	c.664G>A	p.Val222Ile	missense_variant	Exon 6 of 20	1		ENSP00000431657.1	E9PK47
PYGL	ENST00000544180.6 link	c.562G>A	p.Val188Ile	missense_variant	Exon 5 of 19	2		ENSP00000443787.1	P06737-2
PYGL	ENST00000553872.1 link	n.465G>A		non_coding_transcript_exon_variant	Exon 1 of 3	5

Frequencies

GnomAD3 genomes

AF:

0.0950

AC:

14451

AN:

152086

Hom.:

924

Cov.:

show subpopulations

Gnomad AFR

AF:

0.185

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.0484

Gnomad ASJ

AF:

0.0866

Gnomad EAS

AF:

0.0164

Gnomad SAS

AF:

0.0865

Gnomad FIN

AF:

0.0546

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0649

Gnomad OTH

AF:

0.0786

GnomAD3 exomes

AF:

0.0694

AC:

17431

AN:

251334

Hom.:

835

AF XY:

0.0693

AC XY:

9416

AN XY:

135830

show subpopulations

Gnomad AFR exome

AF:

0.189

Gnomad AMR exome

AF:

0.0315

Gnomad ASJ exome

AF:

0.0942

Gnomad EAS exome

AF:

0.00745

Gnomad SAS exome

AF:

0.0923

Gnomad FIN exome

AF:

0.0532

Gnomad NFE exome

AF:

0.0685

Gnomad OTH exome

AF:

0.0697

GnomAD4 exome

AF:

0.0651

AC:

94945

AN:

1458038

Hom.:

3682

Cov.:

AF XY:

0.0662

AC XY:

48018

AN XY:

725638

show subpopulations

Gnomad4 AFR exome

AF:

0.185

Gnomad4 AMR exome

AF:

0.0342

Gnomad4 ASJ exome

AF:

0.0903

Gnomad4 EAS exome

AF:

0.0357

Gnomad4 SAS exome

AF:

0.0931

Gnomad4 FIN exome

AF:

0.0566

Gnomad4 NFE exome

AF:

0.0614

Gnomad4 OTH exome

AF:

0.0657

GnomAD4 genome

AF:

0.0950

AC:

14463

AN:

152204

Hom.:

925

Cov.:

AF XY:

0.0929

AC XY:

6916

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.0483

Gnomad4 ASJ

AF:

0.0866

Gnomad4 EAS

AF:

0.0164

Gnomad4 SAS

AF:

0.0865

Gnomad4 FIN

AF:

0.0546

Gnomad4 NFE

AF:

0.0649

Gnomad4 OTH

AF:

0.0773

Alfa

AF:

0.0694

Hom.:

971

Bravo

AF:

0.0966

TwinsUK

AF:

0.0566

AC:

210

ALSPAC

AF:

0.0545

AC:

210

ESP6500AA

AF:

0.183

AC:

807

ESP6500EA

AF:

0.0649

AC:

558

ExAC

AF:

0.0759

AC:

9219

Asia WGS

AF:

0.0530

AC:

183

AN:

3478

EpiCase

AF:

0.0653

EpiControl

AF:

0.0694

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Apr 14, 2017

Mayo Clinic Laboratories, Mayo Clinic

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

May 05, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Glycogen storage disease, type VI

Benign:2

Jan 12, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.23

BayesDel_noAF

Uncertain

0.030

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.29

.;.;T

Eigen

Benign

0.13

Eigen_PC

Uncertain

0.30

FATHMM_MKL

Uncertain

0.91

LIST_S2

Uncertain

0.93

D;D;D

MetaRNN

Benign

0.0018

T;T;T

MetaSVM

Benign

-0.93

MutationAssessor

Benign

1.8

.;.;L

PrimateAI

Uncertain

0.49

PROVEAN

Benign

-0.86

N;N;N

REVEL

Uncertain

0.38

Sift

Benign

0.11

T;T;T

Sift4G

Benign

0.25

T;T;T

Polyphen

0.016

B;.;B

Vest4

0.066

MPC

0.097

ClinPred

0.025

GERP RS

5.8

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.29

gMVP

0.57

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over