5-55161011-C-G

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong

The NM_001008397.4(GPX8):​c.222C>G​(p.Asn74Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

GPX8
NM_001008397.4 missense

Scores

7
7
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 5.84
Variant links:
Genes affected
GPX8 (HGNC:33100): (glutathione peroxidase 8 (putative)) Enables peroxidase activity. Predicted to be involved in cellular response to oxidative stress. Predicted to be located in endoplasmic reticulum lumen. [provided by Alliance of Genome Resources, Apr 2022]
CDC20B (HGNC:24222): (cell division cycle 20B) Predicted to enable anaphase-promoting complex binding activity and ubiquitin ligase activator activity. Predicted to be involved in anaphase-promoting complex-dependent catabolic process and positive regulation of anaphase-promoting complex-dependent catabolic process. Predicted to be part of anaphase-promoting complex. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.98

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GPX8NM_001008397.4 linkc.222C>G p.Asn74Lys missense_variant Exon 2 of 3 ENST00000503787.6 NP_001008398.2 Q8TED1
CDC20BNM_001170402.1 linkc.126+11577G>C intron_variant Intron 2 of 11 ENST00000381375.7 NP_001163873.1 Q86Y33-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GPX8ENST00000503787.6 linkc.222C>G p.Asn74Lys missense_variant Exon 2 of 3 1 NM_001008397.4 ENSP00000423822.1 Q8TED1
CDC20BENST00000381375.7 linkc.126+11577G>C intron_variant Intron 2 of 11 1 NM_001170402.1 ENSP00000370781.2 Q86Y33-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Apr 07, 2022
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.222C>G (p.N74K) alteration is located in exon 2 (coding exon 2) of the GPX8 gene. This alteration results from a C to G substitution at nucleotide position 222, causing the asparagine (N) at amino acid position 74 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Benign
-0.020
T
BayesDel_noAF
Benign
-0.27
CADD
Pathogenic
32
DANN
Uncertain
1.0
DEOGEN2
Benign
0.28
T;T
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
0.97
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.94
D;D
M_CAP
Benign
0.076
D
MetaRNN
Pathogenic
0.98
D;D
MetaSVM
Uncertain
-0.26
T
MutationAssessor
Pathogenic
4.1
H;.
PrimateAI
Uncertain
0.73
T
PROVEAN
Pathogenic
-5.9
D;D
REVEL
Uncertain
0.49
Sift
Pathogenic
0.0
D;D
Sift4G
Uncertain
0.0060
D;D
Polyphen
1.0
D;D
Vest4
0.98
MutPred
0.93
Gain of methylation at N74 (P = 0.0036);.;
MVP
0.65
MPC
1.3
ClinPred
1.0
D
GERP RS
5.7
Varity_R
0.97
gMVP
0.90

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.10
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr5-54456839; API