4-185144992-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_001151.4(SLC25A4):c.340G>C(p.Ala114Pro) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A114T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001151.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A4 | NM_001151.4 | c.340G>C | p.Ala114Pro | missense_variant | 2/4 | ENST00000281456.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A4 | ENST00000281456.11 | c.340G>C | p.Ala114Pro | missense_variant | 2/4 | 1 | NM_001151.4 | P1 | |
SLC25A4 | ENST00000491736.1 | c.340G>C | p.Ala114Pro | missense_variant, NMD_transcript_variant | 2/4 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 04, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at