rs768312331
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001394028.1(PYY):c.178A>G(p.Thr60Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,460,196 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_001394028.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PYY | NM_001394028.1 | c.178A>G | p.Thr60Ala | missense_variant | Exon 2 of 4 | ENST00000692052.1 | NP_001380957.1 | |
PYY | NM_004160.6 | c.178A>G | p.Thr60Ala | missense_variant | Exon 5 of 7 | NP_004151.4 | ||
PYY | NM_001394029.1 | c.178A>G | p.Thr60Ala | missense_variant | Exon 2 of 3 | NP_001380958.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PYY | ENST00000692052.1 | c.178A>G | p.Thr60Ala | missense_variant | Exon 2 of 4 | NM_001394028.1 | ENSP00000509262.1 | |||
PYY | ENST00000360085.6 | c.178A>G | p.Thr60Ala | missense_variant | Exon 5 of 7 | 1 | ENSP00000353198.1 | |||
PYY | ENST00000592796.2 | c.178A>G | p.Thr60Ala | missense_variant | Exon 2 of 3 | 1 | ENSP00000467310.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000204 AC: 5AN: 245214Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133564
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1460196Hom.: 0 Cov.: 49 AF XY: 0.00000551 AC XY: 4AN XY: 726402
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.178A>G (p.T60A) alteration is located in exon 5 (coding exon 1) of the PYY gene. This alteration results from a A to G substitution at nucleotide position 178, causing the threonine (T) at amino acid position 60 to be replaced by an alanine (A). 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