rs199769855
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_181332.3(NLGN4X):c.955C>T(p.Arg319Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000165 in 1,209,893 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes 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. Synonymous variant affecting the same amino acid position (i.e. R319R) has been classified as Likely benign.
Frequency
Consequence
NM_181332.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN4X | NM_181332.3 | c.955C>T | p.Arg319Trp | missense_variant | 5/6 | ENST00000381095.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN4X | ENST00000381095.8 | c.955C>T | p.Arg319Trp | missense_variant | 5/6 | 1 | NM_181332.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111632Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33816
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1098261Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 1AN XY: 363619
GnomAD4 genome ? AF: 0.00000896 AC: 1AN: 111632Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33816
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at