rs72653759
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1PM5PP3_Strong
The NM_001171.6(ABCC6):c.1091C>T(p.Thr364Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000161 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T364R) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001171.6 missense
Scores
Clinical Significance
Conservation
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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.1091C>T | p.Thr364Met | missense_variant | 9/31 | ENST00000205557.12 | |
ABCC6 | NM_001351800.1 | c.749C>T | p.Thr250Met | missense_variant | 9/31 | ||
ABCC6 | NR_147784.1 | n.1128C>T | non_coding_transcript_exon_variant | 9/29 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ABCC6 | ENST00000205557.12 | c.1091C>T | p.Thr364Met | missense_variant | 9/31 | 1 | NM_001171.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251156Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135736
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461668Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727144
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152206Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at