20-38725074-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate
The NM_080552.3(SLC32A1):c.350C>A(p.Thr117Lys) variant causes a missense change involving the alteration of a conserved nucleotide. 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: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SLC32A1
NM_080552.3 missense
NM_080552.3 missense
Scores
6
7
5
Clinical Significance
Conservation
PhyloP100: 7.71
Publications
0 publications found
Genes affected
SLC32A1 (HGNC:11018): (solute carrier family 32 member 1) The protein encoded by this gene is an integral membrane protein involved in gamma-aminobutyric acid (GABA) and glycine uptake into synaptic vesicles. The encoded protein is a member of amino acid/polyamine transporter family II. [provided by RefSeq, Jul 2008]
SLC32A1 Gene-Disease associations (from GenCC):
- developmental and epileptic encephalopathy 114Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, G2P
- generalized epilepsy with febrile seizures plus, type 12Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 6 curated pathogenic missense variants (we use a threshold of 10). The gene has 1 curated benign missense variants. Gene score misZ: 2.3023 (below the threshold of 3.09). Trascript score misZ: 3.4509 (above the threshold of 3.09). GenCC associations: The gene is linked to developmental and epileptic encephalopathy 114.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.866
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_080552.3. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1365466Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 669194
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1365466
Hom.:
Cov.:
31
AF XY:
AC XY:
0
AN XY:
669194
African (AFR)
AF:
AC:
0
AN:
30070
American (AMR)
AF:
AC:
0
AN:
29956
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
20006
East Asian (EAS)
AF:
AC:
0
AN:
38080
South Asian (SAS)
AF:
AC:
0
AN:
70518
European-Finnish (FIN)
AF:
AC:
0
AN:
48950
Middle Eastern (MID)
AF:
AC:
0
AN:
5306
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1066410
Other (OTH)
AF:
AC:
0
AN:
56170
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Pathogenic
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
N
REVEL
Uncertain
Sift
Benign
D
Sift4G
Uncertain
D
Polyphen
D
Vest4
MutPred
Gain of ubiquitination at T117 (P = 0.0192)
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
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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