chr6-28533967-T-C
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001509.3(GPX5):āc.466T>Cā(p.Cys156Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,426,552 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.000011 ( 0 hom. )
Consequence
GPX5
NM_001509.3 missense
NM_001509.3 missense
Scores
6
7
5
Clinical Significance
Conservation
PhyloP100: 7.00
Genes affected
GPX5 (HGNC:4557): (glutathione peroxidase 5) This gene belongs to the glutathione peroxidase family. It is specifically expressed in the epididymis in the mammalian male reproductive tract, and is androgen-regulated. Unlike several other characterized glutathione peroxidases, this enzyme is not a selenoprotein, lacking the selenocysteine residue. Thus, it is selenium-independent, and has been proposed to play a role in protecting the membranes of spermatozoa from the damaging effects of lipid peroxidation and/or preventing premature acrosome reaction. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.788
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GPX5 | NM_001509.3 | c.466T>C | p.Cys156Arg | missense_variant | 5/5 | ENST00000412168.7 | |
GPX5 | NM_003996.3 | c.*45T>C | 3_prime_UTR_variant | 4/4 | |||
GPX5 | NR_144470.2 | n.544T>C | non_coding_transcript_exon_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GPX5 | ENST00000412168.7 | c.466T>C | p.Cys156Arg | missense_variant | 5/5 | 1 | NM_001509.3 | P1 | |
GPX5 | ENST00000469384.1 | c.*45T>C | 3_prime_UTR_variant | 4/4 | 1 | ||||
GPX5 | ENST00000442674.6 | n.841T>C | non_coding_transcript_exon_variant | 6/6 | 5 | ||||
GPX5 | ENST00000483784.1 | n.539T>C | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000442 AC: 1AN: 226248Hom.: 0 AF XY: 0.00000818 AC XY: 1AN XY: 122224
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GnomAD4 exome AF: 0.0000105 AC: 15AN: 1426552Hom.: 0 Cov.: 29 AF XY: 0.00000990 AC XY: 7AN XY: 707092
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 19, 2024 | The c.466T>C (p.C156R) alteration is located in exon 5 (coding exon 5) of the GPX5 gene. This alteration results from a T to C substitution at nucleotide position 466, causing the cysteine (C) at amino acid position 156 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
M_CAP
Benign
D
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Benign
T
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of disorder (P = 0.0091);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at