Genetic Variant DPEP1:p.Glu351Lys (chr16-89637957-GAG-AAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001389466.1(DPEP1):c.1051_1053delGAGinsAAA(p.Glu351Lys) 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.

Frequency

Genomes: not found (cov: 32)

Consequence

DPEP1
NM_001389466.1 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0150

Publications

0 publications found

Variant links:

Genes affected

DPEP1 (HGNC:3002): (dipeptidase 1) The protein encoded by this gene is a kidney membrane enzyme involved in the metabolism of glutathione and other similar proteins by dipeptide hydrolysis. The encoded protein is known to regulate leukotriene activity by catalyzing the conversion of leukotriene D4 to leukotriene E4. This protein uses zinc as a cofactor and acts as a disulfide-linked homodimer. [provided by RefSeq, Dec 2020]

DPEP1 links:

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new If you want to explore the variant's impact on the transcript NM_001389466.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001389466.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DPEP1	NM_001389466.1	MANE Select	c.1051_1053delGAGinsAAA	p.Glu351Lys	missense	N/A	NP_001376395.1	P16444
DPEP1	NM_001128141.3		c.1051_1053delGAGinsAAA	p.Glu351Lys	missense	N/A	NP_001121613.1	A0A140VJI3
DPEP1	NM_001389467.1		c.1051_1053delGAGinsAAA	p.Glu351Lys	missense	N/A	NP_001376396.1	P16444

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
DPEP1	ENST00000690203.1	MANE Select	c.1051_1053delGAGinsAAA	p.Glu351Lys	missense	N/A	ENSP00000508584.1	P16444
DPEP1	ENST00000261615.5	TSL:1	c.1051_1053delGAGinsAAA	p.Glu351Lys	missense	N/A	ENSP00000261615.4	P16444
DPEP1	ENST00000393092.7	TSL:1	c.1051_1053delGAGinsAAA	p.Glu351Lys	missense	N/A	ENSP00000376807.3	P16444

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.015

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over