rs1386206620
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001191061.2(SLC25A22):c.85A>T(p.Ile29Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00000567 in 1,588,088 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000035 ( 0 hom. )
Consequence
SLC25A22
NM_001191061.2 missense
NM_001191061.2 missense
Scores
3
10
6
Clinical Significance
Conservation
PhyloP100: 4.08
Genes affected
SLC25A22 (HGNC:19954): (solute carrier family 25 member 22) This gene encodes a mitochondrial glutamate carrier. Mutations in this gene are associated with early infantile epileptic encephalopathy. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Jul 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC25A22 | NM_001191061.2 | c.85A>T | p.Ile29Phe | missense_variant | 3/10 | ENST00000628067.3 | NP_001177990.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC25A22 | ENST00000628067.3 | c.85A>T | p.Ile29Phe | missense_variant | 3/10 | 1 | NM_001191061.2 | ENSP00000486058.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000975 AC: 2AN: 205078Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 109918
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GnomAD4 exome AF: 0.00000348 AC: 5AN: 1435882Hom.: 0 Cov.: 32 AF XY: 0.00000141 AC XY: 1AN XY: 711578
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GnomAD4 genome AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74366
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 04, 2022 | This sequence change replaces isoleucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 29 of the SLC25A22 protein (p.Ile29Phe). This variant is present in population databases (no rsID available, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with SLC25A22-related conditions. ClinVar contains an entry for this variant (Variation ID: 461380). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.;.;.;.;.;.;.;.;T;T;T;.;.;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Benign
N;N;N;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;D;D;.;D;.;D;D;D;D;D;D;.;D;D;.;D;D
REVEL
Uncertain
Sift
Uncertain
D;.;D;D;.;D;.;D;D;D;D;D;D;.;D;D;.;D;D
Sift4G
Benign
T;T;T;T;T;.;T;T;D;.;D;.;.;.;.;.;.;.;.
Polyphen
D;D;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
MutPred
Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);Gain of catalytic residue at I29 (P = 0.1601);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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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