rs121909657
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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
ENST00000261937.11 missense
Scores
9
8
2
Clinical Significance
Conservation
PhyloP100: 7.90
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]
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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 |
---|---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.2563G>A | p.Ala855Thr | missense_variant | 18/30 | 1 | NM_182925.5 | ENSP00000261937 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000919 AC: 14AN: 152268Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.00000820 AC: 2AN: 243830Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132808
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1459956Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 726282
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GnomAD4 genome AF: 0.0000919 AC: 14AN: 152386Hom.: 0 Cov.: 34 AF XY: 0.0000805 AC XY: 6AN XY: 74522
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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 provided | literature only | OMIM | Jun 01, 2009 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Sep 13, 2023 | Variant 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 submitter | clinical testing | GeneDx | Sep 01, 2023 | Observed 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
D;.;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Benign
N;N;.
MutationTaster
Benign
A;A;A
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
D;.;D
Vest4
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at