chr2-238250598-C-T

Variant summary

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

The NM_022817.3(PER2):​c.3420G>A​(p.Met1140Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

PER2
NM_022817.3 missense

Scores

1
7
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 4.69
Variant links:
Genes affected
PER2 (HGNC:8846): (period circadian regulator 2) This gene is a member of the Period family of genes and is expressed in a circadian pattern in the suprachiasmatic nucleus, the primary circadian pacemaker in the mammalian brain. Genes in this family encode components of the circadian rhythms of locomotor activity, metabolism, and behavior. This gene is upregulated by CLOCK/ARNTL heterodimers but then represses this upregulation in a feedback loop using PER/CRY heterodimers to interact with CLOCK/ARNTL. Polymorphisms in this gene may increase the risk of getting certain cancers and have been linked to sleep disorders. [provided by RefSeq, Jan 2014]

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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=0.23708051).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PER2NM_022817.3 linkc.3420G>A p.Met1140Ile missense_variant Exon 21 of 23 ENST00000254657.8 NP_073728.1 O15055-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PER2ENST00000254657.8 linkc.3420G>A p.Met1140Ile missense_variant Exon 21 of 23 1 NM_022817.3 ENSP00000254657.3 O15055-1
PER2ENST00000707129.1 linkc.3420G>A p.Met1140Ile missense_variant Exon 21 of 23 ENSP00000516757.1 O15055-1
PER2ENST00000707130.1 linkc.3420G>A p.Met1140Ile missense_variant Exon 21 of 23 ENSP00000516758.1 O15055-1
ENSG00000225057ENST00000456601.1 linkn.1524+3081C>T intron_variant Intron 5 of 6 2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461570
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
727072
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:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.51
BayesDel_addAF
Benign
-0.18
T
BayesDel_noAF
Benign
-0.50
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.15
T
Eigen
Uncertain
0.26
Eigen_PC
Uncertain
0.34
FATHMM_MKL
Uncertain
0.92
D
LIST_S2
Uncertain
0.95
D
M_CAP
Benign
0.0081
T
MetaRNN
Benign
0.24
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Pathogenic
3.0
M
PrimateAI
Benign
0.37
T
PROVEAN
Uncertain
-2.5
N
REVEL
Benign
0.075
Sift
Benign
0.20
T
Sift4G
Benign
0.25
T
Polyphen
0.67
P
Vest4
0.38
MutPred
0.35
Loss of catalytic residue at M1140 (P = 3e-04);
MVP
0.26
MPC
0.32
ClinPred
0.99
D
GERP RS
4.6
Varity_R
0.59
gMVP
0.49

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: chr2-239159239; COSMIC: COSV104542621; API