5-180304776-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_005110.4(GFPT2):c.1838G>A(p.Arg613His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,611,974 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R613C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005110.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GFPT2 | NM_005110.4 | c.1838G>A | p.Arg613His | missense_variant | Exon 17 of 19 | ENST00000253778.13 | NP_005101.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248960Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135074
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1459772Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 726008
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1838G>A (p.R613H) alteration is located in exon 17 (coding exon 17) of the GFPT2 gene. This alteration results from a G to A substitution at nucleotide position 1838, causing the arginine (R) at amino acid position 613 to be replaced by a histidine (H). 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