NM_001370198.1:c.1157G>A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001370198.1(DPEP3):c.1157G>A(p.Arg386His) variant causes a missense change. The variant allele was found at a frequency of 0.0000942 in 1,614,220 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R386C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001370198.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DPEP3 | NM_001370198.1 | c.1157G>A | p.Arg386His | missense_variant | Exon 9 of 10 | ENST00000268793.6 | NP_001357127.1 | |
DPEP3 | NM_001129758.2 | c.1154G>A | p.Arg385His | missense_variant | Exon 9 of 10 | NP_001123230.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DPEP3 | ENST00000268793.6 | c.1157G>A | p.Arg386His | missense_variant | Exon 9 of 10 | 1 | NM_001370198.1 | ENSP00000268793.5 | ||
DPEP3 | ENST00000672962.1 | c.1232G>A | p.Arg411His | missense_variant | Exon 9 of 10 | ENSP00000500237.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000191 AC: 48AN: 251462Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135904
GnomAD4 exome AF: 0.0000978 AC: 143AN: 1461876Hom.: 0 Cov.: 31 AF XY: 0.000128 AC XY: 93AN XY: 727236
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74492
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1232G>A (p.R411H) alteration is located in exon 9 (coding exon 9) of the DPEP3 gene. This alteration results from a G to A substitution at nucleotide position 1232, causing the arginine (R) at amino acid position 411 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at