2-69374078-T-C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PM1PM2PM5PP2PP5BP4
The NM_001244710.2(GFPT1):āc.43A>Gā(p.Thr15Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000139 in 1,443,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. T15M) has been classified as Pathogenic.
Frequency
Consequence
NM_001244710.2 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 |
---|---|---|---|---|---|---|---|
GFPT1 | NM_001244710.2 | c.43A>G | p.Thr15Ala | missense_variant | 2/20 | ENST00000357308.9 | |
GFPT1 | NM_002056.4 | c.43A>G | p.Thr15Ala | missense_variant | 2/19 | ||
GFPT1 | XM_017003801.2 | c.118A>G | p.Thr40Ala | missense_variant | 2/20 | ||
GFPT1 | XM_017003802.3 | c.118A>G | p.Thr40Ala | missense_variant | 2/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GFPT1 | ENST00000357308.9 | c.43A>G | p.Thr15Ala | missense_variant | 2/20 | 5 | NM_001244710.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1443362Hom.: 0 Cov.: 25 AF XY: 0.00000139 AC XY: 1AN XY: 719168
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 12 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 11, 2011 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at