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rs1805192

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4

The NM_138711.6(PPARG):c.28C>G(p.Pro10Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

PPARG
NM_138711.6 missense

Scores

7
9

Clinical Significance

risk factor no assertion criteria provided O:4

Conservation

PhyloP100: 4.22
Variant links:
Genes affected
PPARG (HGNC:9236): (peroxisome proliferator activated receptor gamma) This gene encodes a member of the peroxisome proliferator-activated receptor (PPAR) subfamily of nuclear receptors. PPARs form heterodimers with retinoid X receptors (RXRs) and these heterodimers regulate transcription of various genes. Three subtypes of PPARs are known: PPAR-alpha, PPAR-delta, and PPAR-gamma. The protein encoded by this gene is PPAR-gamma and is a regulator of adipocyte differentiation. Additionally, PPAR-gamma has been implicated in the pathology of numerous diseases including obesity, diabetes, atherosclerosis and cancer. Alternatively spliced transcript variants that encode different isoforms have been described. [provided by RefSeq, Jul 2008]

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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;
PP2
Missense variant where missense usually causes diseases, PPARG
BP4
Computational evidence support a benign effect (MetaRNN=0.2985686).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PPARGNM_138711.6 linkuse as main transcriptc.28C>G p.Pro10Ala missense_variant 3/8 ENST00000651735.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PPARGENST00000651735.1 linkuse as main transcriptc.28C>G p.Pro10Ala missense_variant 3/8 NM_138711.6 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
32

ClinVar

Significance: risk factor
Submissions summary: Other:4
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Body mass index, modifier of Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJun 01, 2007- -
Obesity, modifier of Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJun 01, 2007- -
Intimal medial thickness of internal carotid artery, modifier of Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJun 01, 2007- -
Diabetes mellitus, noninsulin-dependent, modifier of Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJun 01, 2007- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
0.011
T
BayesDel_noAF
Benign
-0.22
Cadd
Uncertain
23
Dann
Uncertain
0.99
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.96
D
M_CAP
Benign
0.036
D
MetaRNN
Benign
0.30
T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.70
T
MutationTaster
Benign
1.0
A;A;A;A;A;A;A;A
PrimateAI
Uncertain
0.53
T
PROVEAN
Benign
-1.3
N;N;N;N;.;.;.;D;N;N;D;N;N
REVEL
Benign
0.10
Sift
Uncertain
0.0070
D;D;D;D;.;.;.;D;D;D;D;D;D
Sift4G
Uncertain
0.041
D;D;D;D;.;.;.;T;D;D;T;D;D
Polyphen
0.35, 0.20
.;.;.;.;.;.;.;.;.;.;.;B;B
Vest4
0.67
MutPred
0.26
.;.;.;.;.;.;.;.;.;.;.;.;Loss of glycosylation at T41 (P = 0.048);
MVP
0.54
MPC
0.14
ClinPred
0.74
D
GERP RS
5.8
Varity_R
0.11
gMVP
0.35

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1805192; hg19: chr3-12421238; API