rs775309900

Variant names:

• chr12-2610660-C-A
• rs775309900
• NM_000719.7:c.3678C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-2610660-C-A
• chr12-2610660-C-G
• chr12-2610660-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP2 PP3

The NM_000719.7(CACNA1C):​c.3678C>A​(p.Phe1226Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. F1226F) has been classified as Benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.328

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 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the CACNA1C gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 45 curated pathogenic missense variants (we use a threshold of 10). The gene has 91 curated benign missense variants. Gene score misZ: 6.4654 (above the threshold of 3.09). Trascript score misZ: 7.2674 (above the threshold of 3.09). GenCC associations: The gene is linked to intellectual disability, neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures, Brugada syndrome, long QT syndrome, short QT syndrome, long qt syndrome 8, Timothy syndrome, Brugada syndrome 3.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.833

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.3828C>A	p.Phe1276Leu	missense_variant	Exon 29 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.3843C>A	p.Phe1281Leu	missense_variant	Exon 29 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.3738C>A	p.Phe1246Leu	missense_variant	Exon 29 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.3768C>A	p.Phe1256Leu	missense_variant	Exon 28 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.3768C>A	p.Phe1256Leu	missense_variant	Exon 28 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.3768C>A	p.Phe1256Leu	missense_variant	Exon 28 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.3768C>A	p.Phe1256Leu	missense_variant	Exon 28 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.3753C>A	p.Phe1251Leu	missense_variant	Exon 29 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.3738C>A	p.Phe1246Leu	missense_variant	Exon 29 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3753C>A	p.Phe1251Leu	missense_variant	Exon 29 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.3669C>A	p.Phe1223Leu	missense_variant	Exon 28 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.3678C>A	p.Phe1226Leu	missense_variant	Exon 28 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*2285C>A		non_coding_transcript_exon_variant	Exon 26 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*2285C>A		3_prime_UTR_variant	Exon 26 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1461874 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727236

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.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.29
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.66	D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;.
Eigen	Benign	-0.43
Eigen_PC	Benign	-0.51
FATHMM_MKL	Uncertain	0.95	D
M_CAP	Pathogenic	0.55	D
MetaRNN	Pathogenic	0.83	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Uncertain	2.2	.;.;.;.;.;.;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.;.;.;.
PrimateAI	Pathogenic	0.89	D
PROVEAN	Pathogenic	-5.5	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;.
REVEL	Pathogenic	0.71
Sift	Benign	0.11	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;.
Sift4G	Benign	0.15	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.94, 0.98, 0.98, 0.68, 1.0, 0.97, 1.0, 0.79, 0.98, 0.95, 0.99, 0.99	.;P;D;D;P;D;D;D;D;P;D;D;P;D;P;D;.;D;P;.;.;.;D;.
Vest4		0.85
MutPred		0.43		.;.;.;.;.;.;.;.;.;.;.;Gain of catalytic residue at I1249 (P = 0.0016);Gain of catalytic residue at I1249 (P = 0.0016);.;.;.;.;.;.;.;.;.;.;.;
MVP		0.93
MPC		1.3
ClinPred		0.99	D
GERP RS		-3.6
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		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: rs775309900; hg19: chr12-2719826;