rs80356508
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1PM2PP2PP3_ModeratePP5_Very_Strong
The NM_001457.4(FLNB):c.679G>A(p.Glu227Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,822 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 Pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
FLNB
NM_001457.4 missense
NM_001457.4 missense
Scores
13
4
1
Clinical Significance
Conservation
PhyloP100: 9.95
Genes affected
FLNB (HGNC:3755): (filamin B) This gene encodes a member of the filamin family. The encoded protein interacts with glycoprotein Ib alpha as part of the process to repair vascular injuries. The platelet glycoprotein Ib complex includes glycoprotein Ib alpha, and it binds the actin cytoskeleton. Mutations in this gene have been found in several conditions: atelosteogenesis type 1 and type 3; boomerang dysplasia; autosomal dominant Larsen syndrome; and spondylocarpotarsal synostosis syndrome. Multiple alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 15 ACMG points.
PM1
?
In a domain Calponin-homology (CH) 2 (size 103) in uniprot entity FLNB_HUMAN there are 58 pathogenic changes around while only 0 benign (100%) in NM_001457.4
PM2
?
Very rare variant in population databases, with high coverage;
PP2
?
Missense variant where missense usually causes diseases, FLNB
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.931
PP5
?
Variant 3-58081668-G-A is Pathogenic according to our data. Variant chr3-58081668-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 6405.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-58081668-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLNB | NM_001457.4 | c.679G>A | p.Glu227Lys | missense_variant | 4/46 | ENST00000295956.9 | |
FLNB | NM_001164317.2 | c.679G>A | p.Glu227Lys | missense_variant | 4/47 | ||
FLNB | NM_001164318.2 | c.679G>A | p.Glu227Lys | missense_variant | 4/46 | ||
FLNB | NM_001164319.2 | c.679G>A | p.Glu227Lys | missense_variant | 4/45 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLNB | ENST00000295956.9 | c.679G>A | p.Glu227Lys | missense_variant | 4/46 | 1 | NM_001457.4 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461822Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727230
GnomAD4 exome
AF:
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1
AN:
1461822
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Cov.:
31
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AC XY:
1
AN XY:
727230
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:4Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | May 22, 2023 | This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 227 of the FLNB protein (p.Glu227Lys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Larsen syndrome (PMID: 14991055, 16648377, 16801345). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 6405). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on FLNB protein function. Experimental studies have shown that this missense change affects FLNB function (PMID: 21620354, 22190451, 26491051). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 06, 2023 | Published functional studies suggest a damaging effect due to a defect in the CH2 domain regulatory function resulting from increased binding of the protein to F-actin or the actin cystoskeleton (Daniel et al., 2012; Zhao et al., 2016); Not observed at significant frequency in large population cohorts (gnomAD); 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: 18322662, 19773341, 22190451, 16801345, 16648377, 30916490, 36267862, 33255942, 33195260, 14991055, 26491051) - |
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 01, 2022 | - - |
Larsen syndrome Pathogenic:1Other:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 2007 | - - |
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
M;M;M;M;.
MutationTaster
Benign
A;A;A;A;A;A;A;A
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D
Polyphen
1.0
.;D;D;.;D
Vest4
MutPred
Gain of ubiquitination at E227 (P = 0.0162);Gain of ubiquitination at E227 (P = 0.0162);Gain of ubiquitination at E227 (P = 0.0162);Gain of ubiquitination at E227 (P = 0.0162);.;
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at