NM_000170.3:c.106G>T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_000170.3(GLDC):c.106G>T(p.Asp36Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000738 in 1,354,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D36H) has been classified as Uncertain significance.
Frequency
Consequence
NM_000170.3 missense
Scores
Clinical Significance
Conservation
Publications
- glycine encephalopathyInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Myriad Women’s Health, Labcorp Genetics (formerly Invitae), ClinGen
- glycine encephalopathy 1Inheritance: AR Classification: DEFINITIVE Submitted by: G2P
- infantile glycine encephalopathyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- neonatal glycine encephalopathyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- atypical glycine encephalopathyInheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLDC | ENST00000321612.8 | c.106G>T | p.Asp36Tyr | missense_variant | Exon 1 of 25 | 1 | NM_000170.3 | ENSP00000370737.4 | ||
LINC02851 | ENST00000813373.1 | n.124+468C>A | intron_variant | Intron 1 of 2 | ||||||
LINC02851 | ENST00000813380.1 | n.405+468C>A | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.38e-7 AC: 1AN: 1354182Hom.: 0 Cov.: 32 AF XY: 0.00000150 AC XY: 1AN XY: 667736 show subpopulations
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at