NM_181715.3:c.1883C>T

Variant names:

• chr1-153948308-G-A
• NM_181715.3:c.1883C>T

Variant summary

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

The NM_181715.3(CRTC2):​c.1883C>T​(p.Ser628Phe) variant causes a missense change involving the alteration of a 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: 33)
• Consequence: CRTC2 NM_181715.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 8.69

Genes affected

CRTC2 (HGNC:27301): (CREB regulated transcription coactivator 2) This gene encodes a member of the transducers of regulated cAMP response element-binding protein activity family of transcription coactivators. These proteins promote the transcription of genes targeted by the cAMP response element-binding protein, and therefore play an important role in many cellular processes. Under basal conditions the encoded protein is phosphorylated by AMP-activated protein kinase or the salt-inducible kinases and is sequestered in the cytoplasm. Upon activation by elevated cAMP or calcium, the encoded protein translocates to the nucleus and increases target gene expression. Single nucleotide polymorphisms in this gene may increase the risk of type 2 diabetes. A pseudogene of this gene is located on the long arm of chromosome 5. [provided by RefSeq, Dec 2010]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRTC2	NM_181715.3	c.1883C>T	p.Ser628Phe	missense_variant	Exon 14 of 14	ENST00000368633.2	NP_859066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRTC2	ENST00000368633.2	c.1883C>T	p.Ser628Phe	missense_variant	Exon 14 of 14	1	NM_181715.3	ENSP00000357622.1
CRTC2	ENST00000461638.6	n.*264C>T		non_coding_transcript_exon_variant	Exon 13 of 13	1		ENSP00000434115.2
CRTC2	ENST00000461638.6	n.*264C>T		3_prime_UTR_variant	Exon 13 of 13	1		ENSP00000434115.2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Nov 12, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1883C>T (p.S628F) alteration is located in exon 14 (coding exon 14) of the CRTC2 gene. This alteration results from a C to T substitution at nucleotide position 1883, causing the serine (S) at amino acid position 628 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.63
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Pathogenic	27
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.52	.;D
Eigen	Uncertain	0.65
Eigen_PC	Uncertain	0.65
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Benign	0.048	D
MetaRNN	Uncertain	0.53	D;D
MetaSVM	Benign	-0.73	T
MutationAssessor	Benign	0.66	.;N
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	-2.2	N;N
REVEL	Uncertain	0.33
Sift	Benign	0.29	T;T
Sift4G	Pathogenic	0.0	D;T
Polyphen		1.0	D;D
Vest4		0.81
MutPred		0.31		.;Loss of disorder (P = 0.0034);
MVP		0.41
MPC		0.89
ClinPred		0.88	D
GERP RS		4.7
Varity_R		0.30
gMVP		0.71

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr1-153920784;