rs142921456
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001163678.2(SHOX2):c.760C>T(p.Pro254Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000533 in 1,613,970 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. P254T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001163678.2 missense
Scores
Clinical Significance
Conservation
Publications
- schizophreniaInheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SHOX2 | ENST00000483851.7 | c.760C>T | p.Pro254Ser | missense_variant | Exon 5 of 5 | 2 | NM_001163678.2 | ENSP00000419362.1 | ||
SHOX2 | ENST00000389589.8 | c.868C>T | p.Pro290Ser | missense_variant | Exon 6 of 6 | 1 | ENSP00000374240.4 | |||
SHOX2 | ENST00000441443.6 | c.796C>T | p.Pro266Ser | missense_variant | Exon 5 of 5 | 5 | ENSP00000397099.3 | |||
SHOX2 | ENST00000490689.3 | n.1911C>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000985 AC: 15AN: 152248Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000926 AC: 23AN: 248490 AF XY: 0.0000520 show subpopulations
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461604Hom.: 0 Cov.: 31 AF XY: 0.0000426 AC XY: 31AN XY: 727120 show subpopulations
GnomAD4 genome AF: 0.0000984 AC: 15AN: 152366Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74506 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at