14-78243275-C-T

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

Scores

1
6
3

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 4.99
Variant links:
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
NRXN3NM_001330195.2 linkuse as main transcriptc.182C>T p.Thr61Met missense_variant 2/21 ENST00000335750.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NRXN3ENST00000335750.7 linkuse as main transcriptc.182C>T p.Thr61Met missense_variant 2/215 NM_001330195.2 P1
NRXN3ENST00000634499.2 linkuse as main transcriptc.182C>T p.Thr61Met missense_variant 2/225
NRXN3ENST00000554738.5 linkuse as main transcriptc.182C>T p.Thr61Met missense_variant 1/205 Q9Y4C0-4

Frequencies

GnomAD3 genomes
AF:
0.000151
AC:
23
AN:
152238
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000362
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000196
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000588
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000698
AC:
12
AN:
171866
Hom.:
0
AF XY:
0.0000532
AC XY:
5
AN XY:
94014
show subpopulations
Gnomad AFR exome
AF:
0.000435
Gnomad AMR exome
AF:
0.000108
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000826
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000266
Gnomad OTH exome
AF:
0.000205
GnomAD4 exome
AF:
0.0000468
AC:
66
AN:
1408938
Hom.:
2
Cov.:
30
AF XY:
0.0000444
AC XY:
31
AN XY:
697454
show subpopulations
Gnomad4 AFR exome
AF:
0.000491
Gnomad4 AMR exome
AF:
0.000154
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000990
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000220
Gnomad4 OTH exome
AF:
0.000136
GnomAD4 genome
AF:
0.000151
AC:
23
AN:
152356
Hom.:
0
Cov.:
32
AF XY:
0.000161
AC XY:
12
AN XY:
74510
show subpopulations
Gnomad4 AFR
AF:
0.000361
Gnomad4 AMR
AF:
0.000196
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000588
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000868
Hom.:
0
Bravo
AF:
0.000170
ExAC
AF:
0.0000348
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 providedclinical testingPreventionGenetics, part of Exact SciencesFeb 21, 2024The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Uncertain
-0.020
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.027
T;.
Eigen
Uncertain
0.34
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Uncertain
0.88
D
LIST_S2
Pathogenic
0.98
D;D
MetaRNN
Benign
0.21
T;T
MetaSVM
Benign
-0.38
T
Sift4G
Uncertain
0.027
D;D
Vest4
0.23
GERP RS
5.9
gMVP
0.49

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs772146074; hg19: chr14-78709618; API