Genetic Variant PRXL2C:p.Gly44Arg (chr9-96655152-C-T) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP4

The NM_153698.2(PRXL2C):c.130G>A(p.Gly44Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,312,634 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00021 ( 1 hom. )

Consequence

PRXL2C
NM_153698.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.32

Publications

1 publications found

Variant links:

Genes affected

PRXL2C (HGNC:16881): (peroxiredoxin like 2C) Predicted to enable antioxidant activity. Involved in positive regulation of ERK1 and ERK2 cascade and positive regulation of glycolytic process. [provided by Alliance of Genome Resources, Apr 2022]

PRXL2C links:

ENSG00000294376 (HGNC:):

ENSG00000294376 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.37246174).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_153698.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRXL2C	NM_153698.2	MANE Select	c.130G>A	p.Gly44Arg	missense	Exon 1 of 6	NP_714542.1	Q7RTV5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PRXL2C	ENST00000375234.8	TSL:1 MANE Select	c.130G>A	p.Gly44Arg	missense	Exon 1 of 6	ENSP00000364382.3	Q7RTV5
PRXL2C	ENST00000446045.1	TSL:1	c.51+100G>A		intron	N/A	ENSP00000398933.1	H0Y5J5
PRXL2C	ENST00000946150.1		c.130G>A	p.Gly44Arg	missense	Exon 1 of 6	ENSP00000616209.1

Frequencies

GnomAD3 genomes

AF:

0.000146

AC:

AN:

150880

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000132

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:

0.000296

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000309

AC:

AN:

6482

AF XY:

0.000248

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000737

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.000211

AC:

245

AN:

1161754

Hom.:

Cov.:

AF XY:

0.000218

AC XY:

123

AN XY:

563978

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23192

American (AMR)

AF:

0.0000967

AC:

AN:

10336

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

15468

East Asian (EAS)

AF:

0.00

AC:

AN:

25534

South Asian (SAS)

AF:

0.00

AC:

AN:

42518

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26172

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3152

European-Non Finnish (NFE)

AF:

0.000244

AC:

236

AN:

968916

Other (OTH)

AF:

0.000172

AC:

AN:

46466

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.000146

AC:

AN:

150880

Hom.:

Cov.:

AF XY:

0.000109

AC XY:

AN XY:

73678

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

41210

American (AMR)

AF:

0.000132

AC:

AN:

15140

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3456

East Asian (EAS)

AF:

0.00

AC:

AN:

5124

South Asian (SAS)

AF:

0.00

AC:

AN:

4816

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10226

Middle Eastern (MID)

AF:

0.00

AC:

AN:

310

European-Non Finnish (NFE)

AF:

0.000296

AC:

AN:

67626

Other (OTH)

AF:

0.00

AC:

AN:

2070

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000265

Hom.:

Bravo

AF:

0.000208

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.85

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Benign

-0.16

CADD

Uncertain

(source)

DANN

Uncertain

0.99

DEOGEN2

Benign

0.40

Eigen

Benign

0.11

Eigen_PC

Benign

-0.088

FATHMM_MKL

Benign

0.44

LIST_S2

Benign

0.73

M_CAP

Uncertain

0.19

MetaRNN

Benign

0.37

MetaSVM

Uncertain

-0.22

PhyloP100

1.3

PrimateAI

Pathogenic

0.86

PROVEAN

Pathogenic

-7.0

REVEL

Uncertain

0.39

Sift

Uncertain

0.016

Sift4G

Uncertain

0.028

Polyphen

0.99

Vest4

0.42

MutPred

0.69

Gain of solvent accessibility (P = 0.0042)

MVP

0.54

MPC

0.17

ClinPred

0.77

GERP RS

3.9

PromoterAI

-0.019

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Varity_R

0.63

gMVP

0.81

Mutation Taster

=49/51

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.080

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