rs1555509499
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM2PP3_Strong
The NM_001171.6(ABCC6):c.3074T>C(p.Leu1025Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. L1025L) has been classified as Likely benign.
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.3074T>C | p.Leu1025Pro | missense_variant | 23/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.2732T>C | p.Leu911Pro | missense_variant | 23/31 | ||
ABCC6 | NR_147784.1 | n.2936T>C | non_coding_transcript_exon_variant | 22/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.3074T>C | p.Leu1025Pro | missense_variant | 23/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000622290.5 | c.3074T>C | p.Leu1025Pro | missense_variant, NMD_transcript_variant | 23/32 | 5 | |||
ABCC6 | ENST00000456970.6 | c.*283T>C | 3_prime_UTR_variant, NMD_transcript_variant | 22/29 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460996Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 726790
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74366
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Uncertain:1
Uncertain significance, criteria provided, single submitter | research | PXE International | Feb 02, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at