9-36191096-CCT-TCA

Variant names:

• chr9-36191096-CCT-TCA
• NM_001833.4:c.40_42delCCTinsTCA
• CLTA p.Pro14Ser

Variant summary

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

The NM_001833.4(CLTA):​c.40_42delCCTinsTCA​(p.Pro14Ser) 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. P14A) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CLTA NM_001833.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89
• Publications: 0 publications found

Genes affected

CLTA (HGNC:2090): (clathrin light chain A) Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001833.4. 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
	CLTA	NM_001833.4	MANE Select	c.40_42delCCTinsTCA	p.Pro14Ser	missense	N/A	NP_001824.1	P09496-2
	CLTA	NM_007096.4		c.40_42delCCTinsTCA	p.Pro14Ser	missense	N/A	NP_009027.1	P09496-1
	CLTA	NM_001076677.3		c.40_42delCCTinsTCA	p.Pro14Ser	missense	N/A	NP_001070145.1	P09496-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CLTA	ENST00000345519.10	TSL:1 MANE Select	c.40_42delCCTinsTCA	p.Pro14Ser	missense	N/A	ENSP00000242284.6	P09496-2
	CLTA	ENST00000242285.11	TSL:1	c.40_42delCCTinsTCA	p.Pro14Ser	missense	N/A	ENSP00000242285.6	P09496-1
	CLTA	ENST00000396603.6	TSL:1	c.40_42delCCTinsTCA	p.Pro14Ser	missense	N/A	ENSP00000379848.2	P09496-3

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.9

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: chr9-36191093;