14-64550970-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_172365.3(PPP1R36):c.119C>A(p.Thr40Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,605,346 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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. T40A) has been classified as Uncertain significance.
Frequency
Consequence
NM_172365.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PPP1R36 | ENST00000298705.6 | c.119C>A | p.Thr40Asn | missense_variant | Exon 2 of 12 | 1 | NM_172365.3 | ENSP00000298705.1 | ||
PPP1R36 | ENST00000557202 | c.-335C>A | 5_prime_UTR_variant | Exon 2 of 8 | 5 | ENSP00000452491.1 | ||||
PPP1R36 | ENST00000467261.5 | n.119C>A | non_coding_transcript_exon_variant | Exon 2 of 13 | 5 | ENSP00000435229.1 | ||||
PPP1R36 | ENST00000555645.5 | n.119C>A | non_coding_transcript_exon_variant | Exon 2 of 5 | 4 | ENSP00000451900.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152140Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000323 AC: 8AN: 247616Hom.: 0 AF XY: 0.0000374 AC XY: 5AN XY: 133790
GnomAD4 exome AF: 0.000105 AC: 152AN: 1453206Hom.: 0 Cov.: 27 AF XY: 0.000104 AC XY: 75AN XY: 723206
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152140Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.119C>A (p.T40N) alteration is located in exon 2 (coding exon 2) of the PPP1R36 gene. This alteration results from a C to A substitution at nucleotide position 119, causing the threonine (T) at amino acid position 40 to be replaced by an asparagine (N). 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