NM_001163678.2:c.877G>T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001163678.2(SHOX2):c.877G>T(p.Ala293Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,611,750 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar 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.877G>T | p.Ala293Ser | missense_variant | Exon 5 of 5 | 2 | NM_001163678.2 | ENSP00000419362.1 | ||
SHOX2 | ENST00000389589.8 | c.985G>T | p.Ala329Ser | missense_variant | Exon 6 of 6 | 1 | ENSP00000374240.4 | |||
SHOX2 | ENST00000441443.6 | c.913G>T | p.Ala305Ser | missense_variant | Exon 5 of 5 | 5 | ENSP00000397099.3 | |||
SHOX2 | ENST00000490689.3 | n.2028G>T | non_coding_transcript_exon_variant | Exon 5 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000124 AC: 3AN: 242620 AF XY: 0.00000754 show subpopulations
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1459520Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726006 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74360 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.985G>T (p.A329S) alteration is located in exon 6 (coding exon 6) of the SHOX2 gene. This alteration results from a G to T substitution at nucleotide position 985, causing the alanine (A) at amino acid position 329 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at