rs752834121
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001394028.1(PYY):c.139C>T(p.Arg47Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000685 in 1,460,472 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
PYY
NM_001394028.1 missense
NM_001394028.1 missense
Scores
4
6
8
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.22
Genes affected
PYY (HGNC:9748): (peptide YY) This gene encodes a member of the neuropeptide Y (NPY) family of peptides. The encoded preproprotein is proteolytically processed to generate two alternative peptide products that differ in length by three amino acids. These peptides, secreted by endocrine cells in the gut, exhibit different binding affinities for each of the neuropeptide Y receptors. Binding of the encoded peptides to these receptors mediates regulation of pancreatic secretion, gut mobility and energy homeostasis. Rare variations in this gene could increase susceptibility to obesity and elevated serum levels of the encoded peptides may be associated with anorexia nervosa. [provided by RefSeq, Feb 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| PYY | NM_001394028.1 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 4 | ENST00000692052.1 | NP_001380957.1 | |
| PYY | NM_004160.6 | c.139C>T | p.Arg47Cys | missense_variant | Exon 5 of 7 | NP_004151.4 | ||
| PYY | NM_001394029.1 | c.139C>T | p.Arg47Cys | 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.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 4 | NM_001394028.1 | ENSP00000509262.1 | |||
| PYY | ENST00000360085.6 | c.139C>T | p.Arg47Cys | missense_variant | Exon 5 of 7 | 1 | ENSP00000353198.1 | |||
| PYY | ENST00000592796.2 | c.139C>T | p.Arg47Cys | missense_variant | Exon 2 of 3 | 1 | ENSP00000467310.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1460472Hom.: 0 Cov.: 50 AF XY: 0.00000138 AC XY: 1AN XY: 726580
GnomAD4 exome
AF:
AC:
1
AN:
1460472
Hom.:
Cov.:
50
AF XY:
AC XY:
1
AN XY:
726580
Gnomad4 AFR exome
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
T;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;.
REVEL
Benign
Sift
Pathogenic
D;.
Sift4G
Pathogenic
D;D
Polyphen
P;.
Vest4
MutPred
Loss of disorder (P = 0.0204);Loss of disorder (P = 0.0204);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at