chr14-52274948-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_000953.3(PTGDR):c.1064T>C(p.Met355Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign 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. M355V) has been classified as Likely benign.
Frequency
Consequence
NM_000953.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTGDR | NM_000953.3 | c.1064T>C | p.Met355Thr | missense_variant | 2/2 | ENST00000306051.3 | |
PTGDR | XM_005267891.5 | c.1064T>C | p.Met355Thr | missense_variant | 2/3 | ||
PTGDR | NM_001281469.2 | c.*264T>C | 3_prime_UTR_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTGDR | ENST00000306051.3 | c.1064T>C | p.Met355Thr | missense_variant | 2/2 | 1 | NM_000953.3 | P1 | |
PTGDR | ENST00000553372.1 | c.*264T>C | 3_prime_UTR_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 29, 2023 | The c.1064T>C (p.M355T) alteration is located in exon 2 (coding exon 2) of the PTGDR gene. This alteration results from a T to C substitution at nucleotide position 1064, causing the methionine (M) at amino acid position 355 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.