3-10301300-TAC-CAA

Variant names:

• chr3-10301300-TAC-CAA
• NM_183352.3:c.928_930delGTAinsTTG
• SEC13 p.Val310Leu

Variant summary

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

The NM_183352.3(SEC13):​c.928_930delGTAinsTTG​(p.Val310Leu) variant causes a missense change. 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. V310I) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: SEC13 NM_183352.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.29
• Publications: 0 publications found

Genes affected

SEC13 (HGNC:10697): (SEC13 homolog, nuclear pore and COPII coat complex component) The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_183352.3. 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
	SEC13	NM_183352.3	MANE Select	c.928_930delGTAinsTTG	p.Val310Leu	missense	N/A	NP_899195.1	P55735-1
	SEC13	NM_001136026.3		c.1066_1068delGTAinsTTG	p.Val356Leu	missense	N/A	NP_001129498.1	P55735-3
	SEC13	NM_030673.4		c.937_939delGTAinsTTG	p.Val313Leu	missense	N/A	NP_109598.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEC13	ENST00000350697.8	TSL:1 MANE Select	c.928_930delGTAinsTTG	p.Val310Leu	missense	N/A	ENSP00000312122.4	P55735-1
	SEC13	ENST00000337354.8	TSL:1	c.937_939delGTAinsTTG	p.Val313Leu	missense	N/A	ENSP00000336566.4	P55735-4
	SEC13	ENST00000397109.7	TSL:1	c.886_888delGTAinsTTG	p.Val296Leu	missense	N/A	ENSP00000380298.3	P55735-2

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		5.3

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: chr3-10342984;