rs143631464

Positions:

chr7-83385314-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_012431.3(SEMA3E):c.1855C>T(p.Arg619Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000179 in 1,612,944 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R619H) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00018 ( 0 hom. )

Consequence

SEMA3E
NM_012431.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:4

Conservation

PhyloP100: 5.03

Variant links:

Genes affected

SEMA3E (HGNC:10727): (semaphorin 3E) Semaphorins are a large family of conserved secreted and membrane associated proteins which possess a semaphorin (Sema) domain and a PSI domain (found in plexins, semaphorins and integrins) in the N-terminal extracellular portion. Based on sequence and structural similarities, semaphorins are put into eight classes: invertebrates contain classes 1 and 2, viruses have class V, and vertebrates contain classes 3-7. Semaphorins serve as axon guidance ligands via multimeric receptor complexes, some (if not all) containing plexin proteins. This gene encodes a class 4 semaphorin. This gene encodes a class 3 semaphorin. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, May 2010]

SEMA3E links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.14716998).

BS2

High AC in GnomAd4 at 21 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SEMA3E	NM_012431.3 linkuse as main transcript	c.1855C>T	p.Arg619Cys	missense_variant	16/17	ENST00000643230.2
SEMA3E	NM_001178129.2 linkuse as main transcript	c.1675C>T	p.Arg559Cys	missense_variant	16/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Appris	UniProt
SEMA3E	ENST00000643230.2 linkuse as main transcript	c.1855C>T	p.Arg619Cys	missense_variant	16/17	NM_012431.3	P1	O15041-1
SEMA3E	ENST00000642232.1 linkuse as main transcript	c.1855C>T	p.Arg619Cys	missense_variant	16/17
SEMA3E	ENST00000643441.1 linkuse as main transcript	n.1840C>T		non_coding_transcript_exon_variant	16/17

Frequencies

GnomAD3 genomes

AF:

0.000138

AC:

AN:

151838

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000967

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000221

Gnomad OTH

AF:

0.000481

GnomAD3 exomes

AF:

0.0000757

AC:

AN:

251110

Hom.:

AF XY:

0.0000884

AC XY:

AN XY:

135724

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000150

Gnomad OTH exome

AF:

0.000164

GnomAD4 exome

AF:

0.000183

AC:

268

AN:

1461106

Hom.:

Cov.:

AF XY:

0.000173

AC XY:

126

AN XY:

726876

show subpopulations

Gnomad4 AFR exome

AF:

0.000150

Gnomad4 AMR exome

AF:

0.0000224

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:

0.000231

Gnomad4 OTH exome

AF:

0.0000828

GnomAD4 genome

AF:

0.000138

AC:

AN:

151838

Hom.:

Cov.:

AF XY:

0.000148

AC XY:

AN XY:

74124

show subpopulations

Gnomad4 AFR

AF:

0.0000967

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000221

Gnomad4 OTH

AF:

0.000481

Alfa

AF:

0.000174

Hom.:

Bravo

AF:

0.000128

ESP6500AA

AF:

0.00

AC:

ESP6500EA

AF:

0.000465

AC:

ExAC

AF:

0.0000988

AC:

EpiCase

AF:

0.0000545

EpiControl

AF:

0.0000593

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Uncertain:2

Uncertain significance, no assertion criteria provided	literature only	OMIM	Oct 14, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 27, 2023	Observed in siblings with Kallman syndrome who were also heterozygous for a variant in the CHD7 gene, and observed in a patient with CHARGE syndrome who inherited the variant from an unaffected heterozygous parent (PMID: 25985275, 15235037); Published in vitro functional studies demonstrate a damaging effect on protein function (PMID: 25985275); In silico analysis supports that this missense variant does not alter protein structure/function; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (PMID: 25741868); This variant is associated with the following publications: (PMID: 29144511, 15235037, 25985275) -

CHARGE syndrome

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Mar 02, 2023

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 619 of the SEMA3E protein (p.Arg619Cys). This variant is present in population databases (rs143631464, gnomAD 0.01%). This missense change has been observed in individual(s) with CHARGE syndrome (PMID: 15235037). ClinVar contains an entry for this variant (Variation ID: 221681). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt SEMA3E protein function. Experimental studies have shown that this missense change affects SEMA3E function (PMID: 25985275). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

SEMA3E-related disorder

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 03, 2023

The SEMA3E c.1855C>T variant is predicted to result in the amino acid substitution p.Arg619Cys. This variant has been reported in two siblings with Kallmann syndrome; however, they also had a variant in CHD7 (p.Phe1019Cys) (Cariboni et al. 2015. PubMed ID: 25985275; Xu et al. 2018. PubMed ID: 29144511). It has also been reported in a child with CHARGE syndrome and their unaffected mother (Lalani et al. 2004. PubMed ID: 15235037). In vitro cell culture assays found this variant was unable to protect cells from cell death (Cariboni et al. 2015. PubMed ID: 25985275). 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

AlphaMissense

Benign

0.16

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.52

CADD

Pathogenic

DANN

Uncertain

1.0

DEOGEN2

Benign

0.20

T;T;.;.

Eigen

Uncertain

0.21

Eigen_PC

Uncertain

0.32

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.72

.;T;T;T

M_CAP

Benign

0.042

MetaRNN

Benign

0.15

T;T;T;T

MetaSVM

Benign

-0.97

MutationAssessor

Benign

1.0

L;L;.;.

MutationTaster

Benign

0.99

D;D

PrimateAI

Benign

0.25

PROVEAN

Benign

-1.6

N;.;N;.

REVEL

Benign

0.11

Sift

Uncertain

0.019

D;.;D;.

Sift4G

Uncertain

0.048

D;.;D;.

Polyphen

0.63

P;P;.;.

Vest4

0.76

MVP

0.71

MPC

0.53

ClinPred

0.47

GERP RS

5.5

Varity_R

0.12

gMVP

0.46

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over