rs1057519296
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3PP5
The NM_138773.4(SLC25A46):c.425C>T(p.Thr142Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000126 in 1,592,836 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 Pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. T142T) has been classified as Likely benign.
Frequency
Consequence
NM_138773.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A46 | NM_138773.4 | c.425C>T | p.Thr142Ile | missense_variant | 4/8 | ENST00000355943.8 | |
SLC25A46 | NM_001303249.3 | c.425C>T | p.Thr142Ile | missense_variant | 4/8 | ||
SLC25A46 | NM_001303250.3 | c.152C>T | p.Thr51Ile | missense_variant | 4/8 | ||
SLC25A46 | NR_138151.2 | n.538C>T | non_coding_transcript_exon_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A46 | ENST00000355943.8 | c.425C>T | p.Thr142Ile | missense_variant | 4/8 | 1 | NM_138773.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1440708Hom.: 0 Cov.: 28 AF XY: 0.00000140 AC XY: 1AN XY: 716800
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74302
ClinVar
Submissions by phenotype
Pontocerebellar hypoplasia, type 1E Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 06, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at