rs1555751089
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000222214.10(GCDH):c.1054C>T(p.Gln352Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.000000684 in 1,461,444 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 (★). Synonymous variant affecting the same amino acid position (i.e. Q352Q) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000222214.10 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GCDH | NM_000159.4 | c.1054C>T | p.Gln352Ter | stop_gained | 10/12 | ENST00000222214.10 | NP_000150.1 | |
GCDH | NM_013976.5 | c.1054C>T | p.Gln352Ter | stop_gained | 10/12 | NP_039663.1 | ||
GCDH | NR_102316.1 | n.1217C>T | non_coding_transcript_exon_variant | 10/12 | ||||
GCDH | NR_102317.1 | n.1435C>T | non_coding_transcript_exon_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GCDH | ENST00000222214.10 | c.1054C>T | p.Gln352Ter | stop_gained | 10/12 | 1 | NM_000159.4 | ENSP00000222214 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461444Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727030
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Glutaric aciduria, type 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Oct 27, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at