14-85622223-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_013231.6(FLRT2):​c.709A>T​(p.Ile237Phe) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

FLRT2
NM_013231.6 missense

Scores

7
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.75
Variant links:
Genes affected
FLRT2 (HGNC:3761): (fibronectin leucine rich transmembrane protein 2) This gene encodes a member of the fibronectin leucine rich transmembrane (FLRT) family of cell adhesion molecules, which regulate early embryonic vascular and neural development. The encoded type I transmembrane protein has an extracellular region consisting of an N-terminal leucine-rich repeat domain and a type 3 fibronectin domain, followed by a transmembrane domain and a short C-terminal cytoplasmic tail domain. It functions as both a homophilic cell adhesion molecule and a heterophilic chemorepellent through its interaction with members of the uncoordinated-5 receptor family. Proteolytic removal of the extracellular region controls the migration of neurons in the developing cortex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FLRT2NM_013231.6 linkuse as main transcriptc.709A>T p.Ile237Phe missense_variant 2/2 ENST00000330753.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FLRT2ENST00000330753.6 linkuse as main transcriptc.709A>T p.Ile237Phe missense_variant 2/21 NM_013231.6 P1
FLRT2ENST00000554746.1 linkuse as main transcriptc.709A>T p.Ile237Phe missense_variant 2/21 P1
FLRT2ENST00000682132.1 linkuse as main transcriptc.709A>T p.Ile237Phe missense_variant 2/2 P1
FLRT2ENST00000683129.1 linkuse as main transcriptc.709A>T p.Ile237Phe missense_variant 2/2 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
32

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 GeneticsApr 24, 2023The c.709A>T (p.I237F) alteration is located in exon 2 (coding exon 1) of the FLRT2 gene. This alteration results from a A to T substitution at nucleotide position 709, causing the isoleucine (I) at amino acid position 237 to be replaced by a phenylalanine (F). 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
Uncertain
0.41
BayesDel_addAF
Benign
-0.075
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
22
DANN
Uncertain
0.99
DEOGEN2
Benign
0.17
T;T
Eigen
Benign
-0.13
Eigen_PC
Benign
-0.020
FATHMM_MKL
Uncertain
0.89
D
LIST_S2
Uncertain
0.96
.;D
M_CAP
Benign
0.012
T
MetaRNN
Uncertain
0.57
D;D
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
1.6
L;L
MutationTaster
Benign
1.0
D;D
PrimateAI
Benign
0.41
T
PROVEAN
Benign
-1.9
N;N
REVEL
Benign
0.21
Sift
Uncertain
0.0040
D;D
Sift4G
Uncertain
0.0080
D;D
Polyphen
0.0090
B;B
Vest4
0.65
MutPred
0.61
Loss of ubiquitination at K233 (P = 0.0683);Loss of ubiquitination at K233 (P = 0.0683);
MVP
0.54
MPC
0.75
ClinPred
0.53
D
GERP RS
5.8
Varity_R
0.18
gMVP
0.65

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: chr14-86088567; API