rs121917869
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_012064.4(MIP):c.401A>G(p.Glu134Gly) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E134A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_012064.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIP | NM_012064.4 | c.401A>G | p.Glu134Gly | missense_variant | 2/4 | ENST00000652304.1 | |
MIP | XM_011538354.2 | c.116A>G | p.Glu39Gly | missense_variant | 4/6 | ||
MIP | XM_017019306.2 | c.44A>G | p.Glu15Gly | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIP | ENST00000652304.1 | c.401A>G | p.Glu134Gly | missense_variant | 2/4 | NM_012064.4 | P1 | ||
MIP | ENST00000555551.1 | n.357A>G | non_coding_transcript_exon_variant | 2/3 | 1 | ||||
MIP | ENST00000648442.1 | n.534A>G | non_coding_transcript_exon_variant | 4/6 | |||||
MIP | ENST00000650166.1 | n.290A>G | non_coding_transcript_exon_variant | 3/5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cataract 15 multiple types Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at