rs2640905

Variant names:

• chr1-7835816-C-G
• rs2640905
• NM_001377275.1:c.3269C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001377275.1(PER3):​c.3269C>G​(p.Ser1090Cys) 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. 12/21 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)
• Consequence: PER3 NM_001377275.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.97

Genes affected

PER3 (HGNC:8847): (period circadian regulator 3) 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 have been linked to sleep disorders. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2014]

ACMG classification

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=0.13794234).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PER3	NM_001377275.1	c.3269C>G	p.Ser1090Cys	missense_variant	Exon 20 of 22	ENST00000377532.8	NP_001364204.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PER3	ENST00000377532.8	c.3269C>G	p.Ser1090Cys	missense_variant	Exon 20 of 22	1	NM_001377275.1	ENSP00000366755.3
PER3	ENST00000361923.2	c.3242C>G	p.Ser1081Cys	missense_variant	Exon 19 of 21	1		ENSP00000355031.2
PER3	ENST00000614998.4	c.3212C>G	p.Ser1071Cys	missense_variant	Exon 21 of 23	1		ENSP00000479223.1
PER3	ENST00000613533.4	c.3269C>G	p.Ser1090Cys	missense_variant	Exon 20 of 22	5		ENSP00000482093.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.092
BayesDel_addAF	Benign	-0.23	T
BayesDel_noAF	Benign	-0.57
CADD	Benign	19
DANN	Uncertain	0.99
DEOGEN2	Benign	0.076	.;T;.;T
Eigen	Benign	-0.63
Eigen_PC	Benign	-0.64
FATHMM_MKL	Benign	0.66	D
LIST_S2	Benign	0.49	T;T;.;T
M_CAP	Benign	0.0083	T
MetaRNN	Benign	0.14	T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.6	.;.;.;L
PrimateAI	Benign	0.27	T
PROVEAN	Uncertain	-2.7	.;.;D;D
REVEL	Benign	0.075
Sift	Uncertain	0.014	.;.;D;D
Sift4G	Uncertain	0.011	D;D;D;D
Polyphen		0.020	B;.;B;B
Vest4		0.16
MutPred		0.25		.;.;.;Loss of phosphorylation at S1081 (P = 0.0616);
MVP		0.36
MPC		0.34
ClinPred		0.87	D
GERP RS		2.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.12
gMVP		0.31

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

Other links and lift over

dbSNP: rs2640905; hg19: chr1-7895876;