rs727504011
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PS1_ModeratePM2PM5PP3_Moderate
The ENST00000340941.11(MCCC2):c.1367C>T(p.Ala456Val) variant causes a missense change. The variant allele was found at a frequency of 0.00000434 in 1,613,528 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 Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A456P) has been classified as Likely pathogenic.
Frequency
Consequence
ENST00000340941.11 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MCCC2 | NM_022132.5 | c.1367C>T | p.Ala456Val | missense_variant | 14/17 | ENST00000340941.11 | NP_071415.1 | |
MCCC2 | NM_001363147.1 | c.1253C>T | p.Ala418Val | missense_variant | 13/16 | NP_001350076.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MCCC2 | ENST00000340941.11 | c.1367C>T | p.Ala456Val | missense_variant | 14/17 | 1 | NM_022132.5 | ENSP00000343657 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251406Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135900
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461400Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727064
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152128Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74294
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 03, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at