NM_001365999.1:c.3570C>G
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001365999.1(SZT2):c.3570C>G(p.Val1190Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,154 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V1190V) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
SZT2
NM_001365999.1 synonymous
NM_001365999.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.728
Publications
0 publications found
Genes affected
SZT2 (HGNC:29040): (SZT2 subunit of KICSTOR complex) The protein encoded by this gene is expressed in the brain, predominantly in the parietal and frontal cortex as well as in dorsal root ganglia. It is localized to the peroxisome, and is implicated in resistance to oxidative stress. It likely functions by increasing superoxide dismutase (SOD) activity, but itself has no direct SOD activity. Studies in mice show that this gene confers low seizure threshold, and may also enhance epileptogenesis. [provided by RefSeq, Jun 2011]
SZT2 Gene-Disease associations (from GenCC):
- developmental and epileptic encephalopathy, 18Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina, PanelApp Australia
- genetic developmental and epileptic encephalopathyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- undetermined early-onset epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
BP6
Variant 1-43427417-C-G is Benign according to our data. Variant chr1-43427417-C-G is described in ClinVar as Likely_benign. ClinVar VariationId is 1616176.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.728 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001365999.1. 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 |
|---|---|---|---|---|---|---|---|---|---|
| SZT2 | NM_001365999.1 | MANE Select | c.3570C>G | p.Val1190Val | synonymous | Exon 25 of 72 | NP_001352928.1 | Q5T011-1 | |
| SZT2 | NM_015284.4 | c.3399C>G | p.Val1133Val | synonymous | Exon 24 of 71 | NP_056099.3 | Q5T011-5 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SZT2 | ENST00000634258.3 | TSL:5 MANE Select | c.3570C>G | p.Val1190Val | synonymous | Exon 25 of 72 | ENSP00000489255.1 | Q5T011-1 | |
| SZT2 | ENST00000562955.2 | TSL:5 | c.3399C>G | p.Val1133Val | synonymous | Exon 24 of 71 | ENSP00000457168.1 | Q5T011-5 | |
| SZT2 | ENST00000470139.1 | TSL:2 | n.*437C>G | non_coding_transcript_exon | Exon 16 of 18 | ENSP00000492726.1 | A0A1W2PRY5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000399 AC: 1AN: 250744 AF XY: 0.00000738 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
250744
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461154Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 726806 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1461154
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
726806
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33476
American (AMR)
AF:
AC:
1
AN:
44674
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26060
East Asian (EAS)
AF:
AC:
0
AN:
39688
South Asian (SAS)
AF:
AC:
0
AN:
86134
European-Finnish (FIN)
AF:
AC:
0
AN:
53404
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
2
AN:
1111594
Other (OTH)
AF:
AC:
1
AN:
60356
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.438
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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