rs63749796
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1PM2PP3_ModeratePP5
The NM_001171.6(ABCC6):c.3712G>C(p.Asp1238His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D1238V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ABCC6 | NM_001171.6 | c.3712G>C | p.Asp1238His | missense_variant | 26/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.3370G>C | p.Asp1124His | missense_variant | 26/31 | ||
ABCC6 | NR_147784.1 | n.3374G>C | non_coding_transcript_exon_variant | 24/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.3712G>C | p.Asp1238His | missense_variant | 26/31 | 1 | NM_001171.6 | P1 | |
ABCC6 | ENST00000622290.5 | c.3712G>C | p.Asp1238His | missense_variant, NMD_transcript_variant | 26/32 | 5 | |||
ABCC6 | ENST00000456970.6 | c.*721G>C | 3_prime_UTR_variant, NMD_transcript_variant | 24/29 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Autosomal recessive inherited pseudoxanthoma elasticum Pathogenic:2
Likely pathogenic, no assertion criteria provided | research | PXE International | Mar 01, 2021 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 01, 2004 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at