6-131674172-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005021.5(ENPP3):c.653C>T(p.Pro218Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000044 in 1,545,264 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005021.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENPP3 | NM_005021.5 | c.653C>T | p.Pro218Leu | missense_variant | Exon 8 of 25 | ENST00000357639.8 | NP_005012.2 | |
ENPP3 | XM_017010932.2 | c.422C>T | p.Pro141Leu | missense_variant | Exon 6 of 23 | XP_016866421.1 | ||
ENPP3 | NR_133007.2 | n.736C>T | non_coding_transcript_exon_variant | Exon 8 of 24 | ||||
ENPP3 | XM_011535897.2 | c.-239C>T | upstream_gene_variant | XP_011534199.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152000Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000640 AC: 16AN: 249838Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134964
GnomAD4 exome AF: 0.0000237 AC: 33AN: 1393264Hom.: 0 Cov.: 23 AF XY: 0.0000187 AC XY: 13AN XY: 696992
GnomAD4 genome AF: 0.000230 AC: 35AN: 152000Hom.: 0 Cov.: 32 AF XY: 0.000256 AC XY: 19AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.653C>T (p.P218L) alteration is located in exon 8 (coding exon 8) of the ENPP3 gene. This alteration results from a C to T substitution at nucleotide position 653, causing the proline (P) at amino acid position 218 to be replaced by a leucine (L). 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