12-2053568-CAAT-C
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_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
NM_000719.7 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
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]
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ACMG classification
Classification made for transcript
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
GnomAD3 genomes
Cov.:
31
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
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:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.