rs946173895
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_032968.5(PCDH11X):c.776C>A(p.Pro259Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000954 in 104,804 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000095 ( 0 hom., 0 hem., cov: 19)
Consequence
PCDH11X
NM_032968.5 missense
NM_032968.5 missense
Scores
5
6
6
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.67
Genes affected
PCDH11X (HGNC:8656): (protocadherin 11 X-linked) This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. The encoded protein consists of an extracellular domain containing 7 cadherin repeats, a transmembrane domain and a cytoplasmic tail that differs from those of the classical cadherins. The gene is located in a major X/Y block of homology and its Y homolog, despite divergence leading to coding region changes, is the most closely related cadherin family member. The protein is thought to play a fundamental role in cell-cell recognition essential for the segmental development and function of the central nervous system. Disruption of this gene may be associated with developmental dyslexia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.785
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00000954 AC: 1AN: 104804Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 27542
GnomAD3 genomes
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GnomAD4 exome Cov.: 29
GnomAD4 exome
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29
GnomAD4 genome 0.00000954 AC: 1AN: 104804Hom.: 0 Cov.: 19 AF XY: 0.00 AC XY: 0AN XY: 27542
GnomAD4 genome
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104804
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27542
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;.;.;.;.
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;M;M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N
REVEL
Uncertain
Sift
Benign
D;D;T;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D
Polyphen
D;D;P;D;D;D
Vest4
MutPred
Loss of glycosylation at S257 (P = 0.0744);Loss of glycosylation at S257 (P = 0.0744);Loss of glycosylation at S257 (P = 0.0744);Loss of glycosylation at S257 (P = 0.0744);Loss of glycosylation at S257 (P = 0.0744);Loss of glycosylation at S257 (P = 0.0744);
MVP
MPC
2.3
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at