12-2053568-CAAT-C

Variant names:

• chr12-2053568-CAAT-C
• NM_000719.7:c.7_9delAAT

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PM4_Supporting

The NM_000719.7(CACNA1C):​c.7_9delAAT​(p.Asn3del) variant causes a conservative inframe deletion 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: 31)
• Consequence: CACNA1C NM_000719.7 conservative_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 4.62

Genes affected

CACNA1C (HGNC:1390): (calcium voltage-gated channel subunit alpha1 C) This gene encodes an alpha-1 subunit of a voltage-dependent calcium channel. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. The alpha-1 subunit consists of 24 transmembrane segments and forms the pore through which ions pass into the cell. The calcium channel consists of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. There are multiple isoforms of each of these proteins, either encoded by different genes or the result of alternative splicing of transcripts. The protein encoded by this gene binds to and is inhibited by dihydropyridine. Alternative splicing results in many transcript variants encoding different proteins. Some of the predicted proteins may not produce functional ion channel subunits. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_000719.7. Strenght limited to Supporting due to length of the change: 1aa.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000406454.8	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000347598.9	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000399638.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.7_9delAAT	p.Asn3del	conservative_inframe_deletion	Exon 1 of 46			ENSP00000507309.1
CACNA1C	ENST00000682544.1	c.140-61655_140-61653delAAT		intron_variant	Intron 1 of 49			ENSP00000507184.1
CACNA1C	ENST00000683824.1	c.140-61655_140-61653delAAT		intron_variant	Intron 1 of 47			ENSP00000507867.1
CACNA1C	ENST00000682462.1	c.140-61655_140-61653delAAT		intron_variant	Intron 1 of 46			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.140-61655_140-61653delAAT		intron_variant	Intron 1 of 46			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.140-61655_140-61653delAAT		intron_variant	Intron 1 of 46			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.140-61655_140-61653delAAT		intron_variant	Intron 1 of 46			ENSP00000506882.1
CACNA1C	ENST00000480911.6	n.7_9delAAT		non_coding_transcript_exon_variant	Exon 1 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Cardiovascular phenotype Uncertain:1

Dec 11, 2020

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.7_9delAAT variant (also known as p.N3del) is located in coding exon 1 of the CACNA1C gene. This variant results from an in-frame AAT deletion at nucleotide positions 7 to 9. This results in the in-frame deletion of an asparagine at codon 3. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-2162734;