chr16-16155022-C-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_001171.6(ABCC6):c.3892G>T(p.Val1298Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000000712 in 1,404,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1298I) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001171.6 missense
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 |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.3892G>T | p.Val1298Phe | missense_variant | 28/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.3550G>T | p.Val1184Phe | missense_variant | 28/31 | ||
ABCC6 | NR_147784.1 | n.3554G>T | non_coding_transcript_exon_variant | 26/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.3892G>T | p.Val1298Phe | missense_variant | 28/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000576204.6 | n.755G>T | non_coding_transcript_exon_variant | 1/2 | 5 | ||||
ABCC6 | ENST00000456970.6 | c.*901G>T | 3_prime_UTR_variant, NMD_transcript_variant | 26/29 | 2 | ||||
ABCC6 | ENST00000622290.5 | c.*64G>T | 3_prime_UTR_variant, NMD_transcript_variant | 29/32 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 7.12e-7 AC: 1AN: 1404280Hom.: 0 Cov.: 32 AF XY: 0.00000144 AC XY: 1AN XY: 693408
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Pathogenic:2
Pathogenic, criteria provided, single submitter | research | PXE International | Mar 01, 2021 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2002 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at