chr15-50202637-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003645.4(SLC27A2):āc.839T>Cā(p.Ile280Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000571 in 1,612,108 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 ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I280V) has been classified as Uncertain significance.
Frequency
Consequence
NM_003645.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC27A2 | NM_003645.4 | c.839T>C | p.Ile280Thr | missense_variant | 3/10 | ENST00000267842.10 | |
SLC27A2 | NM_001159629.2 | c.689-2602T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC27A2 | ENST00000267842.10 | c.839T>C | p.Ile280Thr | missense_variant | 3/10 | 1 | NM_003645.4 | P1 | |
SLC27A2 | ENST00000380902.8 | c.689-2602T>C | intron_variant | 1 | |||||
SLC27A2 | ENST00000544960.1 | c.134T>C | p.Ile45Thr | missense_variant | 4/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250694Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135414
GnomAD4 exome AF: 0.0000589 AC: 86AN: 1459888Hom.: 0 Cov.: 31 AF XY: 0.0000510 AC XY: 37AN XY: 725862
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 20, 2023 | The c.839T>C (p.I280T) alteration is located in exon 3 (coding exon 3) of the SLC27A2 gene. This alteration results from a T to C substitution at nucleotide position 839, causing the isoleucine (I) at amino acid position 280 to be replaced by a threonine (T). 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