20-18593800-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_080820.6(DTD1):c.113C>T(p.Thr38Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,338 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_080820.6 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 |
---|---|---|---|---|---|---|---|---|
DTD1 | NM_080820.6 | c.113C>T | p.Thr38Met | missense_variant | Exon 2 of 6 | ENST00000377452.4 | NP_543010.3 | |
DTD1 | NM_001318043.2 | c.113C>T | p.Thr38Met | missense_variant | Exon 2 of 5 | NP_001304972.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DTD1 | ENST00000377452.4 | c.113C>T | p.Thr38Met | missense_variant | Exon 2 of 6 | 1 | NM_080820.6 | ENSP00000366672.4 | ||
ENSG00000284776 | ENST00000618693.4 | c.188C>T | p.Thr63Met | missense_variant | Exon 2 of 5 | 5 | ENSP00000482916.1 | |||
DTD1 | ENST00000494921.2 | c.113C>T | p.Thr38Met | missense_variant | Exon 2 of 5 | 2 | ENSP00000495845.1 | |||
DTD1 | ENST00000647441.1 | n.113C>T | non_coding_transcript_exon_variant | Exon 2 of 7 | ENSP00000493969.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 251050Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135682
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461338Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 726980
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.113C>T (p.T38M) alteration is located in exon 2 (coding exon 2) of the DTD1 gene. This alteration results from a C to T substitution at nucleotide position 113, causing the threonine (T) at amino acid position 38 to be replaced by a methionine (M). 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