rs1057524272
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001365588.1(NLGN4Y):c.1263C>A(p.Asn421Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001365588.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NLGN4Y | NM_001365588.1 | c.1263C>A | p.Asn421Lys | missense_variant | Exon 6 of 7 | ENST00000684976.1 | NP_001352517.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000625 AC: 2AN: 32010Hom.: 0 Cov.: 0 AF XY: 0.0000625 AC XY: 2AN XY: 32010
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000139 AC: 5AN: 359358Hom.: 0 Cov.: 4 AF XY: 0.0000139 AC XY: 5AN XY: 359358
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000625 AC: 2AN: 32010Hom.: 0 Cov.: 0 AF XY: 0.0000625 AC XY: 2AN XY: 32010
ClinVar
Submissions by phenotype
not provided Uncertain:1
The N401K variant in the NLGN4Y gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The N401K variant was not observed in the Exome Aggregation Consortium (ExAC) data set, indicating it is not a common benign variant (Lek et al., 2016). The N401K variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved in mammals. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret N401K as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at