6-131808055-C-CG
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_006208.3(ENPP1):c.26dup(p.Gly10ArgfsTer67) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 151,978 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. A7A) has been classified as Uncertain significance.
Frequency
Consequence
NM_006208.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ENPP1 | NM_006208.3 | c.26dup | p.Gly10ArgfsTer67 | frameshift_variant | 1/25 | ENST00000647893.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENPP1 | ENST00000647893.1 | c.26dup | p.Gly10ArgfsTer67 | frameshift_variant | 1/25 | NM_006208.3 | P1 | ||
ENPP1 | ENST00000486853.1 | n.46dup | non_coding_transcript_exon_variant | 1/4 | 2 | ||||
ENPP1 | ENST00000513998.5 | c.26dup | p.Gly10ArgfsTer67 | frameshift_variant, NMD_transcript_variant | 1/25 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 10972Hom.: 0 Cov.: 28 FAILED QC
GnomAD4 exome AF: 0.0000132 AC: 2AN: 151978Hom.: 0 Cov.: 33 AF XY: 0.0000278 AC XY: 2AN XY: 71964
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000182 AC: 2AN: 10972Hom.: 0 Cov.: 28 AF XY: 0.000183 AC XY: 1AN XY: 5464
ClinVar
Submissions by phenotype
Hypophosphatemic rickets, autosomal recessive, 2;C4551985:Arterial calcification, generalized, of infancy, 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Genomenon, Inc, Genomenon, Inc | Mar 16, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at