rs144211994

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006238.5(PPARD):​c.1126A>G​(p.Thr376Ala) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,864 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

PPARD
NM_006238.5 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.13
Variant links:
Genes affected
PPARD (HGNC:9235): (peroxisome proliferator activated receptor delta) This gene encodes a member of the peroxisome proliferator-activated receptor (PPAR) family. The encoded protein is thought to function as an integrator of transcriptional repression and nuclear receptor signaling. It may inhibit the ligand-induced transcriptional activity of peroxisome proliferator activated receptors alpha and gamma, though evidence for this effect is inconsistent. Expression of this gene in colorectal cancer cells may be variable but is typically relatively low. Knockout studies in mice suggested a role for this protein in myelination of the corpus callosum, lipid metabolism, differentiation, and epidermal cell proliferation. Alternative splicing results in multiple transcript variants encoding distinct protein isoforms. [provided by RefSeq, Aug 2017]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.20436373).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PPARDNM_006238.5 linkc.1126A>G p.Thr376Ala missense_variant Exon 8 of 8 ENST00000360694.8 NP_006229.1 Q03181-1A0A024RCW6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PPARDENST00000360694.8 linkc.1126A>G p.Thr376Ala missense_variant Exon 8 of 8 2 NM_006238.5 ENSP00000353916.3 Q03181-1
PPARDENST00000311565.4 linkc.1126A>G p.Thr376Ala missense_variant Exon 9 of 9 5 ENSP00000310928.4 Q03181-1
PPARDENST00000448077.6 linkc.1009A>G p.Thr337Ala missense_variant Exon 7 of 7 2 ENSP00000414372.2 Q03181-3
PPARDENST00000418635.6 linkc.832A>G p.Thr278Ala missense_variant Exon 6 of 6 2 ENSP00000413314.2 Q03181-4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000205
AC:
3
AN:
1461864
Hom.:
0
Cov.:
31
AF XY:
0.00000275
AC XY:
2
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.043
T
BayesDel_noAF
Benign
-0.30
CADD
Uncertain
24
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.70
.;D;.;D
Eigen
Benign
0.062
Eigen_PC
Benign
0.22
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Benign
0.70
T;T;T;.
M_CAP
Benign
0.011
T
MetaRNN
Benign
0.20
T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.8
.;L;.;L
PrimateAI
Benign
0.44
T
PROVEAN
Benign
-1.1
N;N;N;N
REVEL
Benign
0.16
Sift
Benign
0.087
T;T;T;T
Sift4G
Benign
0.38
T;T;T;T
Polyphen
0.039
.;B;.;B
Vest4
0.15
MutPred
0.44
.;Loss of catalytic residue at R379 (P = 0.4538);.;Loss of catalytic residue at R379 (P = 0.4538);
MVP
0.58
MPC
0.76
ClinPred
0.68
D
GERP RS
5.0
Varity_R
0.19
gMVP
0.061

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-35393656; API