rs111237511

Variant names:

• chr1-181483501-CTTTTTTTTTTTT-C
• rs111237511
• ENST00000367570.6:c.-241_-230delTTTTTTTTTTTT

Your query was ambiguous. Multiple possible variants found:

• chr1-181483501-CTTTTTTTTTTTT-C
• chr1-181483501-CTTTTTTTTTTTT-CTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTTTTTTTT
• chr1-181483501-CTTTTTTTTTTTT-CTTTTTTTTTTTTTTTT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000367570.6(CACNA1E):​c.-241_-230delTTTTTTTTTTTT variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 29)
• Consequence: CACNA1E ENST00000367570.6 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.275
• Publications: 0 publications found

Genes affected

CACNA1E (HGNC:1392): (calcium voltage-gated channel subunit alpha1 E) Voltage-dependent calcium channels are multisubunit complexes consisting of alpha-1, alpha-2, beta, and delta subunits in a 1:1:1:1 ratio. These channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This gene encodes the alpha-1E subunit of the R-type calcium channels, which belong to the 'high-voltage activated' group that maybe involved in the modulation of firing patterns of neurons important for information processing. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2011]

CACNA1E Gene-Disease associations (from GenCC):

• developmental and epileptic encephalopathy, 69

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Illumina, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• genetic developmental and epileptic encephalopathy

  Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
• neurodevelopmental disorder

  Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000367570.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNA1E	NM_001205293.3	MANE Select	c.-243_-232delTTTTTTTTTTTT		upstream_gene	N/A	NP_001192222.1	Q15878-1
	CACNA1E	NM_000721.4		c.-243_-232delTTTTTTTTTTTT		upstream_gene	N/A	NP_000712.2	Q15878-3
	CACNA1E	NM_001205294.2		c.-243_-232delTTTTTTTTTTTT		upstream_gene	N/A	NP_001192223.1	Q15878-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CACNA1E	ENST00000367570.6	TSL:1	c.-241_-230delTTTTTTTTTTTT		5_prime_UTR	Exon 1 of 47	ENSP00000356542.1	Q15878-3
	CACNA1E	ENST00000524607.6	TSL:5	c.435-240_435-229delTTTTTTTTTTTT		intron	N/A	ENSP00000432038.2	E9PIE8
	CACNA1E	ENST00000533229.1	TSL:1	n.194_205delTTTTTTTTTTTT		non_coding_transcript_exon	Exon 1 of 7

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 1

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.28

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs111237511; hg19: chr1-181452637;