rs369762245

Variant names:

• chr4-15040478-C-G
• rs369762245
• NM_001177382.2:c.2191C>G

Your query was ambiguous. Multiple possible variants found:

• chr4-15040478-C-G
• chr4-15040478-C-A
• chr4-15040478-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001177382.2(CPEB2):​c.2191C>G​(p.Arg731Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CPEB2 NM_001177382.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.61
• Publications: 0 publications found

Genes affected

CPEB2 (HGNC:21745): (cytoplasmic polyadenylation element binding protein 2) The protein encoded by this gene is highly similar to cytoplasmic polyadenylation element binding protein (CPEB), an mRNA-binding protein that regulates cytoplasmic polyadenylation of mRNA as a trans factor in oogenesis and spermatogenesis. Studies of the similar gene in mice suggested a possible role of this protein in transcriptionally inactive haploid spermatids. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

C1QTNF7-AS1 (HGNC:40683): (C1QTNF7 antisense RNA 1)

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001177382.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB2	NM_001177382.2	MANE Select	c.2191C>G	p.Arg731Gly	missense	Exon 6 of 12	NP_001170853.1	Q7Z5Q1-9
	CPEB2	NM_001177381.2		c.2110C>G	p.Arg704Gly	missense	Exon 5 of 11	NP_001170852.1	Q7Z5Q1-8
	CPEB2	NM_001177383.2		c.2101C>G	p.Arg701Gly	missense	Exon 5 of 11	NP_001170854.1	A0A5K1VW71

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CPEB2	ENST00000538197.7	TSL:5 MANE Select	c.2191C>G	p.Arg731Gly	missense	Exon 6 of 12	ENSP00000443985.1	Q7Z5Q1-9
	CPEB2	ENST00000382395.8	TSL:1	c.2101C>G	p.Arg701Gly	missense	Exon 5 of 11	ENSP00000371832.4	A0A5K1VW71
	CPEB2	ENST00000507071.6	TSL:1	c.2176+7267C>G		intron	N/A	ENSP00000424084.2	A0A5K1VW93

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 29

GnomAD4 genome Cov.: 32

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Benign	-0.044	T
BayesDel_noAF	Benign	-0.30
CADD	Pathogenic	27
DANN	Uncertain	1.0
Eigen	Uncertain	0.48
Eigen_PC	Uncertain	0.46
FATHMM_MKL	Uncertain	0.86	D
M_CAP	Benign	0.048	D
MetaRNN	Uncertain	0.44	T
MetaSVM	Benign	-0.31	T
PhyloP100		1.6
PrimateAI	Pathogenic	0.79	T
PROVEAN	Uncertain	-2.9	D
REVEL	Benign	0.17
Sift	Uncertain	0.014	D
Sift4G	Benign	0.084	T
Polyphen		0.99	D
Vest4		0.55
MutPred		0.34		Loss of methylation at R731 (P = 0.013)
MVP		0.51
MPC		2.6
ClinPred		0.99	D
GERP RS		4.9
gMVP		0.77
Mutation Taster		=70/30	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs369762245; hg19: chr4-15042102;