19-18768744-C-A

Position:

• chr19-18768744-C-A

Variant summary

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

The NM_015321.3(CRTC1):​c.1271C>A​(p.Ser424Tyr) variant causes a missense change. 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CRTC1 NM_015321.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 5.84

Genes affected

CRTC1 (HGNC:16062): (CREB regulated transcription coactivator 1) Enables cAMP response element binding protein binding activity. Involved in positive regulation of transcription by RNA polymerase II. Located in cytosol; nuclear body; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

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/exons	MANE	Protein	UniProt
CRTC1	NM_015321.3	c.1271C>A	p.Ser424Tyr	missense_variant	10/14	ENST00000321949.13	NP_056136.2
CRTC1	NM_001098482.2	c.1319C>A	p.Ser440Tyr	missense_variant	11/15		NP_001091952.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CRTC1	ENST00000321949.13	c.1271C>A	p.Ser424Tyr	missense_variant	10/14	1	NM_015321.3	ENSP00000323332	A1
CRTC1	ENST00000338797.10	c.1319C>A	p.Ser440Tyr	missense_variant	11/15	1		ENSP00000345001	P4
CRTC1	ENST00000594658.5	c.1148C>A	p.Ser383Tyr	missense_variant	10/14	1		ENSP00000468893
CRTC1	ENST00000601916.1	c.786+3216C>A		intron_variant		5		ENSP00000469285

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1446774 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 718676

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: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 25, 2023

The c.1319C>A (p.S440Y) alteration is located in exon 11 (coding exon 11) of the CRTC1 gene. This alteration results from a C to A substitution at nucleotide position 1319, causing the serine (S) at amino acid position 440 to be replaced by a tyrosine (Y). 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	0.16
BayesDel_addAF	Benign	-0.073	T
BayesDel_noAF	Benign	-0.34
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.38	T;.;.
Eigen	Uncertain	0.40
Eigen_PC	Uncertain	0.41
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Benign	0.81	T;T;T
M_CAP	Benign	0.056	D
MetaRNN	Uncertain	0.48	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.3	M;.;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.71	T
PROVEAN	Benign	-1.7	N;N;.
REVEL	Benign	0.075
Sift	Pathogenic	0.0	D;D;.
Sift4G	Uncertain	0.027	D;D;D
Polyphen		0.92	P;P;.
Vest4		0.65
MutPred		0.17		Loss of glycosylation at S424 (P = 0.0112);.;.;
MVP		0.31
MPC		1.7
ClinPred		0.97	D
GERP RS		4.0
Varity_R		0.32
gMVP		0.62

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		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: chr19-18879554;