rs750612085
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3PP5
The NM_032808.7(LINGO1):āc.863A>Gā(p.Tyr288Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000479 in 1,461,710 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_032808.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LINGO1 | NM_032808.7 | c.863A>G | p.Tyr288Cys | missense_variant | 2/2 | ENST00000355300.7 | NP_116197.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LINGO1 | ENST00000355300.7 | c.863A>G | p.Tyr288Cys | missense_variant | 2/2 | 1 | NM_032808.7 | ENSP00000347451.6 | ||
LINGO1 | ENST00000561030.5 | c.845A>G | p.Tyr282Cys | missense_variant | 4/4 | 1 | ENSP00000453853.1 | |||
LINGO1 | ENST00000557798.1 | c.878A>G | p.Tyr293Cys | missense_variant | 2/2 | 3 | ENSP00000453780.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249434Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135260
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461710Hom.: 0 Cov.: 58 AF XY: 0.00000688 AC XY: 5AN XY: 727138
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Intellectual disability, autosomal recessive 64 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 29, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at