rs104894431
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP3_StrongPP5_Moderate
The NM_014252.4(SLC25A15):c.824G>A(p.Arg275Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,611,900 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R275P) has been classified as Uncertain significance.
Frequency
Consequence
NM_014252.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC25A15 | NM_014252.4 | c.824G>A | p.Arg275Gln | missense_variant | 7/7 | ENST00000338625.9 | |
TPTE2P5 | NR_038259.1 | n.452-8861C>T | intron_variant, non_coding_transcript_variant | ||||
TPTE2P5 | NR_038258.1 | n.623-8861C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC25A15 | ENST00000338625.9 | c.824G>A | p.Arg275Gln | missense_variant | 7/7 | 1 | NM_014252.4 | P1 | |
SLC25A15 | ENST00000707033.1 | c.824G>A | p.Arg275Gln | missense_variant | 7/7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152062Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251140Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135724
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459838Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 726238
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152062Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74262
ClinVar
Submissions by phenotype
Hyperornithinemia-hyperammonemia-homocitrullinuria syndrome Pathogenic:2Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 11, 2001 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Dec 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at