7-123147172-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_022444.4(SLC13A1):c.799G>A(p.Glu267Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000136 in 1,613,464 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E267D) has been classified as Uncertain significance.
Frequency
Consequence
NM_022444.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC13A1 | NM_022444.4 | c.799G>A | p.Glu267Lys | missense_variant | 7/15 | ENST00000194130.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC13A1 | ENST00000194130.7 | c.799G>A | p.Glu267Lys | missense_variant | 7/15 | 1 | NM_022444.4 | P1 | |
SLC13A1 | ENST00000439260.5 | c.*1177G>A | 3_prime_UTR_variant, NMD_transcript_variant | 10/18 | 1 | ||||
SLC13A1 | ENST00000539873.1 | c.*466G>A | 3_prime_UTR_variant | 8/16 | 5 | ||||
SLC13A1 | ENST00000427975.5 | c.*742G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/16 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250300Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135238
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461292Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726930
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 17, 2022 | The c.799G>A (p.E267K) alteration is located in exon 7 (coding exon 7) of the SLC13A1 gene. This alteration results from a G to A substitution at nucleotide position 799, causing the glutamic acid (E) at amino acid position 267 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at