NM_002708.4:c.845T>C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_002708.4(PPP1CA):āc.845T>Cā(p.Met282Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,772 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 (ā ).
Frequency
Consequence
NM_002708.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1CA | NM_002708.4 | c.845T>C | p.Met282Thr | missense_variant | Exon 6 of 7 | ENST00000376745.9 | NP_002699.1 | |
PPP1CA | NM_001008709.2 | c.878T>C | p.Met293Thr | missense_variant | Exon 6 of 7 | NP_001008709.1 | ||
PPP1CA | NM_206873.2 | c.713T>C | p.Met238Thr | missense_variant | Exon 5 of 6 | NP_996756.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251158Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135852
GnomAD4 exome AF: 0.00000410 AC: 6AN: 1461694Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727134
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.878T>C (p.M293T) alteration is located in exon 6 (coding exon 6) of the PPP1CA gene. This alteration results from a T to C substitution at nucleotide position 878, causing the methionine (M) at amino acid position 293 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