chrX-91877898-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_032968.5(PCDH11X):c.1658A>C(p.Asn553Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N553D) has been classified as Uncertain significance.
Frequency
Consequence
NM_032968.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCDH11X | NM_032968.5 | c.1658A>C | p.Asn553Thr | missense_variant | 6/11 | ENST00000682573.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCDH11X | ENST00000682573.1 | c.1658A>C | p.Asn553Thr | missense_variant | 6/11 | NM_032968.5 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 20
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2022 | The c.1658A>C (p.N553T) alteration is located in exon 2 (coding exon 2) of the PCDH11X gene. This alteration results from a A to C substitution at nucleotide position 1658, causing the asparagine (N) at amino acid position 553 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.