chr7-134933241-GAA-CAG

Variant names:

• chr7-134933241-GAA-CAG
• NM_033138.4:c.472_474delGAAinsCAG
• CALD1 p.Glu158Gln

Variant summary

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

The NM_033138.4(CALD1):​c.472_474delGAAinsCAG​(p.Glu158Gln) variant causes a missense 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 MNV, 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E158K) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 30)
• Consequence: CALD1 NM_033138.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.23
• Publications: 0 publications found

Genes affected

CALD1 (HGNC:1441): (caldesmon 1) This gene encodes a calmodulin- and actin-binding protein that plays an essential role in the regulation of smooth muscle and nonmuscle contraction. The conserved domain of this protein possesses the binding activities to Ca(2+)-calmodulin, actin, tropomyosin, myosin, and phospholipids. This protein is a potent inhibitor of the actin-tropomyosin activated myosin MgATPase, and serves as a mediating factor for Ca(2+)-dependent inhibition of smooth muscle contraction. Alternative splicing of this gene results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008]

ENSG00000286458 (HGNC:):

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_033138.4. 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
	CALD1	NM_033138.4	MANE Select	c.472_474delGAAinsCAG	p.Glu158Gln	missense	N/A	NP_149129.2
	CALD1	NM_001438765.1		c.472_474delGAAinsCAG	p.Glu158Gln	missense	N/A	NP_001425694.1
	CALD1	NM_001438766.1		c.454_456delGAAinsCAG	p.Glu152Gln	missense	N/A	NP_001425695.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CALD1	ENST00000361675.7	TSL:1 MANE Select	c.472_474delGAAinsCAG	p.Glu158Gln	missense	N/A	ENSP00000354826.2	Q05682-1
	CALD1	ENST00000393118.7	TSL:1	c.454_456delGAAinsCAG	p.Glu152Gln	missense	N/A	ENSP00000376826.2	Q05682-3
	CALD1	ENST00000361901.6	TSL:1	c.472_474delGAAinsCAG	p.Glu158Gln	missense	N/A	ENSP00000354513.2	Q05682-4

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-134617992;