16-67977334-CAC-TAG

Variant names:

• chr16-67977334-CAC-TAG
• NM_001370198.1:c.952_954delGTGinsCTA
• DPEP3 p.Val318Leu

Variant summary

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

The NM_001370198.1(DPEP3):​c.952_954delGTGinsCTA​(p.Val318Leu) 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. V318M) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: DPEP3 NM_001370198.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.62
• Publications: 0 publications found

Genes affected

DPEP3 (HGNC:23029): (dipeptidase 3) This gene encodes a membrane-bound glycoprotein from the family of dipeptidases involved in hydrolytic metabolism of various dipeptides, including penem and carbapenem beta-lactam antibiotics. This gene is located on chromosome 16 in a cluster with another member of this family. Alternatively spliced transcript variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370198.1. 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
	DPEP3	NM_001370198.1	MANE Select	c.952_954delGTGinsCTA	p.Val318Leu	missense	N/A	NP_001357127.1	Q9H4B8
	DPEP3	NM_001129758.2		c.949_951delGTGinsCTA	p.Val317Leu	missense	N/A	NP_001123230.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPEP3	ENST00000268793.6	TSL:1 MANE Select	c.952_954delGTGinsCTA	p.Val318Leu	missense	N/A	ENSP00000268793.5	Q9H4B8
	DPEP3	ENST00000672962.1		c.1027_1029delGTGinsCTA	p.Val343Leu	missense	N/A	ENSP00000500237.1	A0A5F9ZHB4
	DPEP3	ENST00000876631.1		c.949_951delGTGinsCTA	p.Val317Leu	missense	N/A	ENSP00000546690.1

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		5.6

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: chr16-68011237;