15-90629447-C-T

Variant names:

• chr15-90629447-C-T
• rs1968958271
• NM_022769.5:c.1181C>T

Variant summary

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

The NM_022769.5(CRTC3):​c.1181C>T​(p.Thr394Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,872 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: CRTC3 NM_022769.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 6.06

Genes affected

CRTC3 (HGNC:26148): (CREB regulated transcription coactivator 3) This gene is a member of the CREB regulated transcription coactivator gene family. This family regulates CREB-dependent gene transcription in a phosphorylation-independent manner and may be selective for cAMP-responsive genes. The protein encoded by this gene may induce mitochondrial biogenesis and attenuate catecholamine signaling in adipose tissue. A translocation event between this gene and Notch coactivator mastermind-like gene 2, which results in a fusion protein, has been reported in mucoepidermoid carcinomas. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, Jul 2012]

CRTC3-AS1 (HGNC:51433): (CRTC3 antisense RNA 1)

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
CRTC3	NM_022769.5	c.1181C>T	p.Thr394Met	missense_variant	Exon 11 of 15	ENST00000268184.11	NP_073606.3
CRTC3	NM_001042574.3	c.1181C>T	p.Thr394Met	missense_variant	Exon 11 of 15		NP_001036039.1
CRTC3-AS1	NR_120372.1	n.510-9294G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CRTC3	ENST00000268184.11	c.1181C>T	p.Thr394Met	missense_variant	Exon 11 of 15	1	NM_022769.5	ENSP00000268184.6
CRTC3	ENST00000420329.6	c.1181C>T	p.Thr394Met	missense_variant	Exon 11 of 15	2		ENSP00000416573.2
CRTC3	ENST00000686240.1	n.*594C>T		non_coding_transcript_exon_variant	Exon 10 of 14			ENSP00000508866.1
CRTC3	ENST00000691029.1	n.1181C>T		non_coding_transcript_exon_variant	Exon 11 of 17			ENSP00000510507.1
CRTC3	ENST00000692149.1	n.*508C>T		non_coding_transcript_exon_variant	Exon 9 of 13			ENSP00000510448.1
CRTC3	ENST00000686240.1	n.*594C>T		3_prime_UTR_variant	Exon 10 of 14			ENSP00000508866.1
CRTC3	ENST00000692149.1	n.*508C>T		3_prime_UTR_variant	Exon 9 of 13			ENSP00000510448.1
CRTC3	ENST00000687075.1	n.*417C>T		downstream_gene_variant				ENSP00000510590.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000342 AC: 5 AN: 1461872 Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2 AN XY: 727240

Gnomad4 AFR exome AF: 0.0000299

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: 0.00000360

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

Bravo AF: 0.0000113

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Aug 17, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1181C>T (p.T394M) alteration is located in exon 11 (coding exon 11) of the CRTC3 gene. This alteration results from a C to T substitution at nucleotide position 1181, causing the threonine (T) at amino acid position 394 to be replaced by a methionine (M). 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	Benign	0.32
BayesDel_addAF	Uncertain	0.077	D
BayesDel_noAF	Benign	-0.13
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.31	.;T
Eigen	Uncertain	0.58
Eigen_PC	Uncertain	0.51
FATHMM_MKL	Uncertain	0.97	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Benign	0.014	T
MetaRNN	Uncertain	0.52	D;D
MetaSVM	Benign	-1.1	T
MutationAssessor	Uncertain	2.8	M;M
PrimateAI	Uncertain	0.68	T
PROVEAN	Uncertain	-2.7	D;D
REVEL	Benign	0.16
Sift	Uncertain	0.0010	D;D
Sift4G	Uncertain	0.038	D;D
Polyphen		1.0	D;D
Vest4		0.62
MutPred		0.15		Loss of phosphorylation at T394 (P = 0.0308);Loss of phosphorylation at T394 (P = 0.0308);
MVP		0.14
MPC		0.31
ClinPred		0.98	D
GERP RS		5.2
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.23
gMVP		0.60

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: rs1968958271; hg19: chr15-91172679; COSMIC: COSV51598829; COSMIC: COSV51598829;