rs121909657

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PP3_Moderate

The ENST00000261937.11(FLT4):​c.2563G>A​(p.Ala855Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,612,342 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: 𝑓 0.000092 ( 0 hom., cov: 34)
Exomes 𝑓: 0.0000075 ( 0 hom. )

Consequence

FLT4
ENST00000261937.11 missense

Scores

9
8
2

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts P:1U:2

Conservation

PhyloP100: 7.90
Variant links:
Genes affected
FLT4 (HGNC:3767): (fms related receptor tyrosine kinase 4) This gene encodes a tyrosine kinase receptor for vascular endothelial growth factors C and D. The protein is thought to be involved in lymphangiogenesis and maintenance of the lymphatic endothelium. Mutations in this gene cause hereditary lymphedema type IA. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM1
In a binding_site (size 8) in uniprot entity VGFR3_HUMAN there are 11 pathogenic changes around while only 0 benign (100%) in ENST00000261937.11
PP3
MetaRNN computational evidence supports a deleterious effect, 0.908

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FLT4NM_182925.5 linkuse as main transcriptc.2563G>A p.Ala855Thr missense_variant 18/30 ENST00000261937.11 NP_891555.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FLT4ENST00000261937.11 linkuse as main transcriptc.2563G>A p.Ala855Thr missense_variant 18/301 NM_182925.5 ENSP00000261937 P1P35916-2

Frequencies

GnomAD3 genomes
AF:
0.0000919
AC:
14
AN:
152268
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000850
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00000820
AC:
2
AN:
243830
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
132808
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000167
GnomAD4 exome
AF:
0.00000753
AC:
11
AN:
1459956
Hom.:
0
Cov.:
32
AF XY:
0.00000688
AC XY:
5
AN XY:
726282
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.000112
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:
0.00000270
Gnomad4 OTH exome
AF:
0.0000497
GnomAD4 genome
AF:
0.0000919
AC:
14
AN:
152386
Hom.:
0
Cov.:
34
AF XY:
0.0000805
AC XY:
6
AN XY:
74522
show subpopulations
Gnomad4 AFR
AF:
0.0000240
Gnomad4 AMR
AF:
0.000849
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.000178
ExAC
AF:
0.00000825
AC:
1

ClinVar

Significance: Uncertain significance
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Hereditary lymphedema type I Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyOMIMJun 01, 2009- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingWomen's Health and Genetics/Laboratory Corporation of America, LabCorpSep 13, 2023Variant summary: FLT4 c.2563G>A (p.Ala855Thr) results in a non-conservative amino acid change located in the protein kinase domain (IPR000719) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8.2e-06 in 243830 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2563G>A has been reported in the literature in a homozygous proband affected with lymphoedema from a consanguineous family. However, parents who were heterozygous for this variant had no clinical signs of lymphoedema indicating variant did not segregate with disease in this family (example: Ghalamkarpour_2009). This report does not provide unequivocal conclusions about association of the variant with FLT4-Related Disorders. One publication reports experimental evidence that phosphorylation of the A855T mutant FLT4/VEGFR3 is weak upon VEGF-C induction. However, this report does not allow convincing conclusions about the variant effect (example: Ghalamkarpour_2009). The following publication has been ascertained in the context of this evaluation (PMID: 19289394). No submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance. -
not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingGeneDxSep 01, 2023Observed in the homozygous state in a patient in published literature with congenital lymphedema whose heterozygous parents were unaffected, and not observed in the homozygous state in controls (Ghalamkarpour et al., 2009); Published functional studies suggest a damaging effect: impaired ligand induced internalization, impaired ERK1/2 activity, and reduced receptor phosphorylation (Ghalamkarpour et al., 2009); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 10835628, 11114740, 23074044, 19289394) -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.92
BayesDel_addAF
Pathogenic
0.25
D
BayesDel_noAF
Pathogenic
0.21
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.66
D;.;D
Eigen
Uncertain
0.33
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.97
D;D;D
M_CAP
Pathogenic
0.78
D
MetaRNN
Pathogenic
0.91
D;D;D
MetaSVM
Uncertain
0.68
D
MutationAssessor
Benign
0.64
N;N;.
MutationTaster
Benign
1.0
A;A;A
PrimateAI
Uncertain
0.73
T
PROVEAN
Uncertain
-3.4
D;D;D
REVEL
Pathogenic
0.82
Sift
Pathogenic
0.0
D;D;D
Sift4G
Pathogenic
0.0
D;D;D
Polyphen
1.0
D;.;D
Vest4
0.81
MVP
0.78
MPC
1.6
ClinPred
0.99
D
GERP RS
3.4
Varity_R
0.84
gMVP
0.83

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: rs121909657; hg19: chr5-180046749; API