Genetic Variant PLPBP:p.Val24Met (chr8-37762729-G-A) – 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_007198.4(PLPBP):c.70G>A(p.Val24Met) variant causes a missense change. The variant allele was found at a frequency of 0.00173 in 1,585,556 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V24E) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0093 ( 26 hom., cov: 32)

Exomes 𝑓: 0.00093 ( 15 hom. )

Consequence

PLPBP
NM_007198.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 4.61

Publications

4 publications found

Variant links:

Genes affected

PLPBP (HGNC:9457): (pyridoxal phosphate binding protein) This gene encodes a pyridoxal 5'-phosphate binding protein involved in the homeostatic regulation of intracellular pyridoxal 5'-phosphate. This gene has a tumor suppressive effect on hepatocellular carcinoma and other solid tumors of epithelial origin. Naturally occurring mutations in this gene are associated with a pyridoxine-dependent epilepsy. [provided by RefSeq, Mar 2017]

PLPBP Gene-Disease associations (from GenCC):

epilepsy, early-onset, vitamin B6-dependent
Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
pyridoxine-dependent epilepsy
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

PLPBP links:

ENSG00000304882 (HGNC:):

ENSG00000304882 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=0.007576108).

BP6

Variant 8-37762729-G-A is Benign according to our data. Variant chr8-37762729-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 445758.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00934 (1422/152286) while in subpopulation AFR AF = 0.0327 (1357/41558). AF 95% confidence interval is 0.0312. There are 26 homozygotes in GnomAd4. There are 664 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 26 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007198.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PLPBP	NM_007198.4	MANE Select	c.70G>A	p.Val24Met	missense	Exon 1 of 8	NP_009129.1	O94903
PLPBP	NM_001349346.2		c.70G>A	p.Val24Met	missense	Exon 1 of 8	NP_001336275.1
PLPBP	NM_001349347.2		c.70G>A	p.Val24Met	missense	Exon 1 of 8	NP_001336276.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PLPBP	ENST00000328195.8	TSL:1 MANE Select	c.70G>A	p.Val24Met	missense	Exon 1 of 8	ENSP00000333551.3	O94903
PLPBP	ENST00000872272.1		c.70G>A	p.Val24Met	missense	Exon 1 of 8	ENSP00000542331.1
PLPBP	ENST00000958638.1		c.70G>A	p.Val24Met	missense	Exon 1 of 8	ENSP00000628697.1

Frequencies

GnomAD3 genomes

AF:

0.00914

AC:

1391

AN:

152168

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0320

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.00574

GnomAD2 exomes

AF:

0.00215

AC:

428

AN:

198810

AF XY:

0.00159

show subpopulations

Gnomad AFR exome

AF:

0.0298

Gnomad AMR exome

AF:

0.00161

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000678

Gnomad OTH exome

AF:

0.000588

GnomAD4 exome

AF:

0.000925

AC:

1326

AN:

1433270

Hom.:

Cov.:

AF XY:

0.000811

AC XY:

577

AN XY:

711322

show subpopulations

African (AFR)

AF:

0.0317

AC:

1054

AN:

33206

American (AMR)

AF:

0.00143

AC:

AN:

41142

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25594

East Asian (EAS)

AF:

0.00

AC:

AN:

38910

South Asian (SAS)

AF:

0.000217

AC:

AN:

82968

European-Finnish (FIN)

AF:

0.00

AC:

AN:

43812

Middle Eastern (MID)

AF:

0.00240

AC:

AN:

5000

European-Non Finnish (NFE)

AF:

0.0000354

AC:

AN:

1103156

Other (OTH)

AF:

0.00242

AC:

144

AN:

59482

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.482

Heterozygous variant carriers

142

212

283

354

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.00934

AC:

1422

AN:

152286

Hom.:

Cov.:

AF XY:

0.00892

AC XY:

664

AN XY:

74468

show subpopulations

African (AFR)

AF:

0.0327

AC:

1357

AN:

41558

American (AMR)

AF:

0.00287

AC:

AN:

15306

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5160

South Asian (SAS)

AF:

0.00

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000132

AC:

AN:

68028

Other (OTH)

AF:

0.00568

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

145

217

290

362

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

100

<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:

0.0471

Hom.:

2356

Bravo

AF:

0.0102

ESP6500AA

AF:

0.0260

AC:

113

ESP6500EA

AF:

0.000118

AC:

ExAC

AF:

0.00214

AC:

253

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.28

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.39

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.16

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.43

FATHMM_MKL

Benign

0.66

LIST_S2

Benign

0.78

MetaRNN

Benign

0.0076

MetaSVM

Benign

-0.97

PhyloP100

4.6

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-2.0

REVEL

Benign

0.14

Sift

Benign

0.11

Sift4G

Benign

0.17

Polyphen

0.96

Vest4

0.40

MVP

0.65

MPC

0.56

ClinPred

0.068

GERP RS

4.6

PromoterAI

0.025

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Varity_R

0.21

gMVP

0.67

Mutation Taster

=84/16

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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