10-81875485-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001010848.4(NRG3):​c.145C>T​(p.Pro49Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000746 in 1,341,098 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 7.5e-7 ( 0 hom. )

Consequence

NRG3
NM_001010848.4 missense

Scores

1
3
15

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.511
Variant links:
Genes affected
NRG3 (HGNC:7999): (neuregulin 3) This gene is a member of the neuregulin gene family. This gene family encodes ligands for the transmembrane tyrosine kinase receptors ERBB3 and ERBB4 - members of the epidermal growth factor receptor family. Ligand binding activates intracellular signaling cascades and the induction of cellular responses including proliferation, migration, differentiation, and survival or apoptosis. This gene encodes neuregulin 3 (NRG3). NRG3 has been shown to activate the tyrosine phosphorylation of its cognate receptor, ERBB4, and is thought to influence neuroblast proliferation, migration and differentiation by signalling through ERBB4. NRG3 also promotes mammary differentiation during embryogenesis. Linkage studies have implicated this gene as a susceptibility locus for schizophrenia and schizoaffective disorder. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional transcript variants have been described but their biological validity has not been verified.[provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25142005).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
NRG3NM_001010848.4 linkuse as main transcriptc.145C>T p.Pro49Ser missense_variant 1/9 ENST00000372141.7 NP_001010848.2 P56975-4B9EGV5

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
NRG3ENST00000372141.7 linkuse as main transcriptc.145C>T p.Pro49Ser missense_variant 1/91 NM_001010848.4 ENSP00000361214.2 P56975-4
NRG3ENST00000404547.5 linkuse as main transcriptc.145C>T p.Pro49Ser missense_variant 1/101 ENSP00000384796.1 P56975-1

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
7.46e-7
AC:
1
AN:
1341098
Hom.:
0
Cov.:
31
AF XY:
0.00000152
AC XY:
1
AN XY:
659120
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000183
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsDec 16, 2023The c.145C>T (p.P49S) alteration is located in exon 1 (coding exon 1) of the NRG3 gene. This alteration results from a C to T substitution at nucleotide position 145, causing the proline (P) at amino acid position 49 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.20
T
BayesDel_noAF
Benign
-0.53
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.27
.;T
Eigen
Benign
-0.17
Eigen_PC
Benign
-0.14
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.61
T;T
M_CAP
Uncertain
0.23
D
MetaRNN
Benign
0.25
T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.55
N;N
PrimateAI
Pathogenic
0.92
D
PROVEAN
Benign
-1.0
N;N
REVEL
Benign
0.030
Sift
Uncertain
0.0050
D;D
Sift4G
Benign
0.22
T;T
Polyphen
0.53
P;.
Vest4
0.43
MutPred
0.22
Gain of phosphorylation at P49 (P = 0.0662);Gain of phosphorylation at P49 (P = 0.0662);
MVP
0.52
MPC
0.56
ClinPred
0.49
T
GERP RS
2.4
Varity_R
0.15
gMVP
0.15

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr10-83635241; API