14-78243275-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_001330195.2(NRXN3):c.182C>T(p.Thr61Met) variant causes a missense change. The variant allele was found at a frequency of 0.000057 in 1,561,294 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.00015 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000047 ( 2 hom. )
Consequence
NRXN3
NM_001330195.2 missense
NM_001330195.2 missense
Scores
1
6
3
Clinical Significance
Conservation
PhyloP100: 4.99
Genes affected
NRXN3 (HGNC:8010): (neurexin 3) This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants and protein isoforms for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. Genetic variation at this locus has been associated with a range of behavioral phenotypes, including alcohol dependence and autism spectrum disorder. [provided by RefSeq, Dec 2012]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), NRXN3. . Gene score misZ 3.438 (greater than the threshold 3.09). Trascript score misZ 4.1674 (greater than threshold 3.09). GenCC has associacion of gene with autism.
BP4
Computational evidence support a benign effect (MetaRNN=0.20626312).
BS2
High AC in GnomAd4 at 23 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRXN3 | NM_001330195.2 | c.182C>T | p.Thr61Met | missense_variant | 2/21 | ENST00000335750.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRXN3 | ENST00000335750.7 | c.182C>T | p.Thr61Met | missense_variant | 2/21 | 5 | NM_001330195.2 | P1 | |
NRXN3 | ENST00000634499.2 | c.182C>T | p.Thr61Met | missense_variant | 2/22 | 5 | |||
NRXN3 | ENST00000554738.5 | c.182C>T | p.Thr61Met | missense_variant | 1/20 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152238Hom.: 0 Cov.: 32
GnomAD3 genomes
AF:
AC:
23
AN:
152238
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.0000698 AC: 12AN: 171866Hom.: 0 AF XY: 0.0000532 AC XY: 5AN XY: 94014
GnomAD3 exomes
AF:
AC:
12
AN:
171866
Hom.:
AF XY:
AC XY:
5
AN XY:
94014
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000468 AC: 66AN: 1408938Hom.: 2 Cov.: 30 AF XY: 0.0000444 AC XY: 31AN XY: 697454
GnomAD4 exome
AF:
AC:
66
AN:
1408938
Hom.:
Cov.:
30
AF XY:
AC XY:
31
AN XY:
697454
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.000151 AC: 23AN: 152356Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74510
GnomAD4 genome
AF:
AC:
23
AN:
152356
Hom.:
Cov.:
32
AF XY:
AC XY:
12
AN XY:
74510
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ExAC
AF:
AC:
4
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
NRXN3-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2024 | The NRXN3 c.182C>T variant is predicted to result in the amino acid substitution p.Thr61Met. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.039% of alleles in individuals of African descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
Sift4G
Uncertain
D;D
Vest4
GERP RS
gMVP
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