rs72653776
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3PP5
The NM_001171.6(ABCC6):c.1781C>T(p.Ala594Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00000411 in 1,460,982 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. A594A) has been classified as Likely benign.
Frequency
Consequence
NM_001171.6 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.1781C>T | p.Ala594Val | missense_variant, splice_region_variant | 14/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.1439C>T | p.Ala480Val | missense_variant, splice_region_variant | 14/31 | ||
ABCC6 | NR_147784.1 | n.1818C>T | splice_region_variant, non_coding_transcript_exon_variant | 14/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1781C>T | p.Ala594Val | missense_variant, splice_region_variant | 14/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000622290.5 | c.1781C>T | p.Ala594Val | missense_variant, splice_region_variant, NMD_transcript_variant | 14/32 | 5 | |||
ABCC6 | ENST00000456970.6 | c.1781C>T | p.Ala594Val | missense_variant, splice_region_variant, NMD_transcript_variant | 14/29 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248598Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134738
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460982Hom.: 0 Cov.: 36 AF XY: 0.00000550 AC XY: 4AN XY: 726762
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | PXE International | Mar 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at