2-144007185-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_001376312.2(GTDC1):c.872G>A(p.Arg291Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000216 in 1,574,098 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 (★).
Frequency
Consequence
NM_001376312.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GTDC1 | NM_001376312.2 | c.872G>A | p.Arg291Lys | missense_variant | Exon 7 of 12 | ENST00000682281.1 | NP_001363241.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000133 AC: 3AN: 225504Hom.: 0 AF XY: 0.0000166 AC XY: 2AN XY: 120606
GnomAD4 exome AF: 0.0000225 AC: 32AN: 1422018Hom.: 0 Cov.: 28 AF XY: 0.0000156 AC XY: 11AN XY: 703480
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.872G>A (p.R291K) alteration is located in exon 7 (coding exon 4) of the GTDC1 gene. This alteration results from a G to A substitution at nucleotide position 872, causing the arginine (R) at amino acid position 291 to be replaced by a lysine (K). 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