rs746346104
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_181303.2(NLGN3):c.2353C>T(p.Arg785Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,197,425 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 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. R785H) has been classified as Uncertain significance.
Frequency
Consequence
NM_181303.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NLGN3 | NM_181303.2 | c.2353C>T | p.Arg785Cys | missense_variant | 8/8 | ENST00000358741.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NLGN3 | ENST00000358741.4 | c.2353C>T | p.Arg785Cys | missense_variant | 8/8 | 5 | NM_181303.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000542 AC: 6AN: 110742Hom.: 0 Cov.: 22 AF XY: 0.0000303 AC XY: 1AN XY: 32996
GnomAD3 exomes AF: 0.0000128 AC: 2AN: 156778Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 48936
GnomAD4 exome AF: 0.0000138 AC: 15AN: 1086630Hom.: 0 Cov.: 32 AF XY: 0.00000845 AC XY: 3AN XY: 355208
GnomAD4 genome ? AF: 0.0000451 AC: 5AN: 110795Hom.: 0 Cov.: 22 AF XY: 0.0000302 AC XY: 1AN XY: 33059
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 23, 2015 | The R765C variant in the NLGN3 gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The R765C variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The R765C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position where amino acids with similar properties to Arginine are tolerated across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret R765C as a variant of uncertain significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Aug 01, 2017 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 15, 2021 | The c.2293C>T (p.R765C) alteration is located in exon 7 (coding exon 6) of the NLGN3 gene. This alteration results from a C to T substitution at nucleotide position 2293, causing the arginine (R) at amino acid position 765 to be replaced by a cysteine (C). 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