rs587780404
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_181332.3(NLGN4X):c.54C>T(p.Cys18Cys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 0.0000018 ( 0 hom. 2 hem. )
Failed GnomAD Quality Control
Consequence
NLGN4X
NM_181332.3 synonymous
NM_181332.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.73
Publications
1 publications found
Genes affected
NLGN4X (HGNC:14287): (neuroligin 4 X-linked) This gene encodes a member of the type-B carboxylesterase/lipase protein family. The encoded protein belongs to a family of neuronal cell surface proteins. Members of this family may act as splice site-specific ligands for beta-neurexins and may be involved in the formation and remodeling of central nervous system synapses. The encoded protein interacts with discs large homolog 4 (DLG4). Mutations in this gene have been associated with autism and Asperger syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
NLGN4X Gene-Disease associations (from GenCC):
- X-linked complex neurodevelopmental disorderInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- autism, susceptibility to, X-linked 2Inheritance: XL Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.81).
BP6
Variant X-6151413-G-A is Benign according to our data. Variant chrX-6151413-G-A is described in ClinVar as [Benign]. Clinvar id is 129805.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=1.73 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| NLGN4X | NM_181332.3 | c.54C>T | p.Cys18Cys | synonymous_variant | Exon 2 of 6 | ENST00000381095.8 | NP_851849.1 |
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000182 AC: 2AN: 1098054Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 2AN XY: 363408 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
2
AN:
1098054
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
363408
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26402
American (AMR)
AF:
AC:
0
AN:
35207
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19386
East Asian (EAS)
AF:
AC:
1
AN:
30204
South Asian (SAS)
AF:
AC:
0
AN:
54146
European-Finnish (FIN)
AF:
AC:
0
AN:
40533
Middle Eastern (MID)
AF:
AC:
0
AN:
4135
European-Non Finnish (NFE)
AF:
AC:
1
AN:
841946
Other (OTH)
AF:
AC:
0
AN:
46095
GnomAD4 genome
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Mar 17, 2014
Genetic Services Laboratory, University of Chicago
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.