7-5528458-C-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1PM2PP2PP3_ModeratePP5_Very_Strong

The NM_001101.5(ACTB):​c.625G>A​(p.Val209Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: not found (cov: 33)

Consequence

ACTB
NM_001101.5 missense

Scores

9
6
3

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:10

Conservation

PhyloP100: 7.62
Variant links:
Genes affected
ACTB (HGNC:132): (actin beta) This gene encodes one of six different actin proteins. Actins are highly conserved proteins that are involved in cell motility, structure, integrity, and intercellular signaling. The encoded protein is a major constituent of the contractile apparatus and one of the two nonmuscle cytoskeletal actins that are ubiquitously expressed. Mutations in this gene cause Baraitser-Winter syndrome 1, which is characterized by intellectual disability with a distinctive facial appearance in human patients. Numerous pseudogenes of this gene have been identified throughout the human genome. [provided by RefSeq, Aug 2017]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 15 ACMG points.

PM1
In a helix (size 13) in uniprot entity ACTB_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_001101.5
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the ACTB gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 94 curated pathogenic missense variants (we use a threshold of 10). The gene has 13 curated benign missense variants. Trascript score misZ: 7.6852 (above the threshold of 3.09). GenCC associations: The gene is linked to ACTB-associated syndromic thrombocytopenia, Baraitser-Winter cerebrofrontofacial syndrome, developmental malformations-deafness-dystonia syndrome, Baraitser-Winter syndrome 1.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.85
PP5
Variant 7-5528458-C-T is Pathogenic according to our data. Variant chr7-5528458-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 127172.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-5528458-C-T is described in Lovd as [Pathogenic]. Variant chr7-5528458-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ACTBNM_001101.5 linkc.625G>A p.Val209Met missense_variant 4/6 ENST00000646664.1 NP_001092.1 P60709Q1KLZ0

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ACTBENST00000646664.1 linkc.625G>A p.Val209Met missense_variant 4/6 NM_001101.5 ENSP00000494750.1 P60709

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
69
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:10
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Baraitser-Winter syndrome 1 Pathogenic:5
Pathogenic, criteria provided, single submitterclinical testingInstitute of Human Genetics Munich, Klinikum Rechts Der Isar, TU MünchenJun 19, 2020- -
Pathogenic, no assertion criteria providedclinical testingDepartment of Genetics, Robert DEBRE University HospitalApr 15, 2014- -
Likely pathogenic, criteria provided, single submitterclinical testingCentogene AG - the Rare Disease Company-- -
Likely pathogenic, criteria provided, single submitterclinical testingGenetic Services Laboratory, University of ChicagoJul 02, 2013- -
Pathogenic, criteria provided, single submitterclinical testingDaryl Scott Lab, Baylor College of MedicineJan 01, 2024PS2, PS4, PM2, PP3 -
not provided Pathogenic:3
Pathogenic, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenFeb 01, 2023ACTB: PS2, PM2, PS4:Moderate, PP2, PP3 -
Pathogenic, criteria provided, single submitterclinical testingGeneDxAug 28, 2024Reported previously as V209L, with the same nucleotide change, in an individual with BWCFF who developed acute lymphoblastic leukemia at age eight (PMID: 25052316); Not observed at significant frequency in large population cohorts (gnomAD); The majority of missense variants in this gene are considered pathogenic; In silico analysis indicates that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 28191890, 30733661, 28991257, 32860008, 34906496, 31941532, 25052316, 32368696) -
Likely pathogenic, criteria provided, single submitterclinical testingInstitute of Medical Genetics and Applied Genomics, University Hospital TübingenOct 23, 2020- -
Inborn genetic diseases Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingAmbry GeneticsMay 23, 2023The c.625G>A (p.V209M) alteration is located in exon 4 (coding exon 3) of the ACTB gene. This alteration results from a G to A substitution at nucleotide position 625, causing the valine (V) at amino acid position 209 to be replaced by a methionine (M)._x000D_ _x000D_ The ACTB c.625G>A (p.V209M) alteration is classified as pathogenic for Baraitser-Winter syndrome; however, its clinical significance for ACTB-related pleiotropic malformation syndrome is unclear. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This alteration, also referred to as c.625G>A (p.V209L), was reported in multiple individuals with features consistent with Baraitser-Winter syndrome (Verloes, 2015; Bertoli-Avella, 2021), including an individual with a de novo occurrence (Jin, 2017; Edwards, 2020; Gonzalez-Teran, 2022). This amino acid position is highly conserved in available vertebrate species. This missense alteration is located in a region that has a low rate of benign missense variation (Lek, 2016; Firth, 2009). The in silico prediction for this alteration is inconclusive. Based on the available evidence, this alteration is classified as pathogenic. -
ACTB-related BAFopathy Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingBaylor GeneticsJun 10, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.99
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.070
CADD
Pathogenic
28
DANN
Benign
0.97
DEOGEN2
Pathogenic
0.89
D;D;D;.;.
Eigen
Uncertain
0.31
Eigen_PC
Uncertain
0.38
FATHMM_MKL
Pathogenic
0.97
D
LIST_S2
Uncertain
0.90
.;.;D;D;D
M_CAP
Pathogenic
0.65
D
MetaRNN
Pathogenic
0.85
D;D;D;D;D
MetaSVM
Uncertain
0.79
D
MutationAssessor
Pathogenic
3.1
M;M;M;.;.
PrimateAI
Pathogenic
0.91
D
PROVEAN
Benign
-2.3
N;.;.;.;.
REVEL
Pathogenic
0.91
Sift4G
Uncertain
0.0080
D;.;.;.;.
Polyphen
0.039
B;B;B;.;.
Vest4
0.90
MutPred
0.73
Gain of disorder (P = 0.1232);Gain of disorder (P = 0.1232);Gain of disorder (P = 0.1232);.;.;
MVP
0.91
MPC
1.8
ClinPred
0.99
D
GERP RS
4.7
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.90
gMVP
0.96

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: rs587779777; hg19: chr7-5568089; API