dbSNP rs56257827: PHKB:p.Met185Ile (chr16-47515562-G-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000293.3(PHKB):c.555G>T(p.Met185Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0109 in 1,504,410 control chromosomes in the GnomAD database, including 146 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0099 ( 17 hom., cov: 32)

Exomes 𝑓: 0.011 ( 129 hom. )

Consequence

PHKB
NM_000293.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1B:12O:1

Conservation

PhyloP100: 8.28

Publications

16 publications found

Variant links:

Genes affected

PHKB (HGNC:8927): (phosphorylase kinase regulatory subunit beta) Phosphorylase kinase is a polymer of 16 subunits, four each of alpha, beta, gamma and delta. The alpha subunit includes the skeletal muscle and hepatic isoforms, encoded by two different genes. The beta subunit is the same in both the muscle and hepatic isoforms, encoded by this gene, which is a member of the phosphorylase b kinase regulatory subunit family. The gamma subunit also includes the skeletal muscle and hepatic isoforms, encoded by two different genes. The delta subunit is a calmodulin and can be encoded by three different genes. The gamma subunits contain the active site of the enzyme, whereas the alpha and beta subunits have regulatory functions controlled by phosphorylation. The delta subunit mediates the dependence of the enzyme on calcium concentration. Mutations in this gene cause glycogen storage disease type 9B, also known as phosphorylase kinase deficiency of liver and muscle. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. Two pseudogenes have been found on chromosomes 14 and 20, respectively.[provided by RefSeq, Feb 2010]

PHKB Gene-Disease associations (from GenCC):

glycogen storage disease IXb
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet, Labcorp Genetics (formerly Invitae), ClinGen

PHKB links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.009557545).

BP6

Variant 16-47515562-G-T is Benign according to our data. Variant chr16-47515562-G-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 198067.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00989 (1505/152220) while in subpopulation NFE AF = 0.013 (886/68002). AF 95% confidence interval is 0.0123. There are 17 homozygotes in GnomAd4. There are 730 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 17 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000293.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PHKB	NM_000293.3	MANE Select	c.555G>T	p.Met185Ile	missense	Exon 6 of 31	NP_000284.1	Q93100-1
PHKB	NM_001363837.1		c.555G>T	p.Met185Ile	missense	Exon 6 of 31	NP_001350766.1	Q93100-3
PHKB	NM_001031835.3		c.534G>T	p.Met178Ile	missense	Exon 7 of 32	NP_001027005.1	Q93100-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PHKB	ENST00000323584.10	TSL:1 MANE Select	c.555G>T	p.Met185Ile	missense	Exon 6 of 31	ENSP00000313504.5	Q93100-1
PHKB	ENST00000566044.5	TSL:1	c.534G>T	p.Met178Ile	missense	Exon 7 of 32	ENSP00000456729.1	Q93100-4
PHKB	ENST00000567402.5	TSL:1	n.570G>T		non_coding_transcript_exon	Exon 6 of 11

Frequencies

GnomAD3 genomes

AF:

0.00989

AC:

1505

AN:

152102

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00234

Gnomad AMI

AF:

0.00440

Gnomad AMR

AF:

0.00713

Gnomad ASJ

AF:

0.0628

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0152

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0130

Gnomad OTH

AF:

0.00860

GnomAD2 exomes

AF:

0.0112

AC:

2799

AN:

250950

AF XY:

0.0109

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00506

Gnomad ASJ exome

AF:

0.0629

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.0113

Gnomad NFE exome

AF:

0.0139

Gnomad OTH exome

AF:

0.0162

GnomAD4 exome

AF:

0.0110

AC:

14830

AN:

1352190

Hom.:

129

Cov.:

AF XY:

0.0108

AC XY:

7309

AN XY:

678838

show subpopulations

African (AFR)

AF:

0.00168

AC:

AN:

31482

American (AMR)

AF:

0.00523

AC:

233

AN:

44590

Ashkenazi Jewish (ASJ)

AF:

0.0628

AC:

1598

AN:

25444

East Asian (EAS)

AF:

0.0000256

AC:

AN:

39056

South Asian (SAS)

AF:

0.00142

AC:

119

AN:

83928

European-Finnish (FIN)

AF:

0.0117

AC:

621

AN:

52886

Middle Eastern (MID)

AF:

0.0131

AC:

AN:

5562

European-Non Finnish (NFE)

AF:

0.0113

AC:

11414

AN:

1012544

Other (OTH)

AF:

0.0127

AC:

718

AN:

56698

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

596

1192

1787

2383

2979

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

408

816

1224

1632

2040

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00989

AC:

1505

AN:

152220

Hom.:

Cov.:

AF XY:

0.00981

AC XY:

730

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.00234

AC:

AN:

41536

American (AMR)

AF:

0.00713

AC:

109

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0628

AC:

218

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5188

South Asian (SAS)

AF:

0.00207

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.0152

AC:

161

AN:

10580

Middle Eastern (MID)

AF:

0.00680

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0130

AC:

886

AN:

68002

Other (OTH)

AF:

0.00851

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

155

233

310

388

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

110

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0133

Hom.:

Bravo

AF:

0.00920

TwinsUK

AF:

0.0156

AC:

ALSPAC

AF:

0.0109

AC:

ESP6500AA

AF:

0.00227

AC:

ESP6500EA

AF:

0.0152

AC:

131

ExAC

AF:

0.0110

AC:

1339

Asia WGS

AF:

0.000869

AC:

AN:

3468

EpiCase

AF:

0.0149

EpiControl

AF:

0.0143

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Glycogen storage disease IXb (6)

not provided (4)

not specified (4)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.92

BayesDel_addAF

Benign

-0.088

BayesDel_noAF

Uncertain

0.11

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Uncertain

0.77

Eigen

Pathogenic

0.84

Eigen_PC

Pathogenic

0.84

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.94

MetaRNN

Benign

0.0096

MetaSVM

Uncertain

0.53

MutationAssessor

Uncertain

2.7

PhyloP100

8.3

PrimateAI

Uncertain

0.77

PROVEAN

Uncertain

-3.6

REVEL

Pathogenic

0.77

Sift

Benign

0.043

Sift4G

Uncertain

0.054

Polyphen

0.98

Vest4

0.70

MutPred

0.85

Gain of catalytic residue at S187 (P = 0.0981)

MPC

0.40

ClinPred

0.012

GERP RS

5.7

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.45

gMVP

0.84

Mutation Taster

=99/1

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

2.0

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over