rs864321716

Variant names:

• chr16-89935236-G-A
• rs864321716
• NM_006086.4:c.785G>A

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_006086.4(TUBB3):​c.785G>A​(p.Arg262His) 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: TUBB3 NM_006086.4 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9 O:1
• Conservation: PhyloP100: 9.82

Genes affected

TUBB3 (HGNC:20772): (tubulin beta 3 class III) This gene encodes a class III member of the beta tubulin protein family. Beta tubulins are one of two core protein families (alpha and beta tubulins) that heterodimerize and assemble to form microtubules. This protein is primarily expressed in neurons and may be involved in neurogenesis and axon guidance and maintenance. Mutations in this gene are the cause of congenital fibrosis of the extraocular muscles type 3. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 6. [provided by RefSeq, Oct 2010]

ENSG00000198211 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the TUBB3 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 45 curated pathogenic missense variants (we use a threshold of 10). The gene has 6 curated benign missense variants. Gene score misZ: 4.5786 (above the threshold of 3.09). Trascript score misZ: 5.665 (above the threshold of 3.09). GenCC associations: The gene is linked to tubulinopathy-associated dysgyria, complex cortical dysplasia with other brain malformations 1, congenital fibrosis of extraocular muscles, fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.994
• PP5: Variant 16-89935236-G-A is Pathogenic according to our data. Variant chr16-89935236-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 219256.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TUBB3	NM_006086.4	c.785G>A	p.Arg262His	missense_variant	Exon 4 of 4	ENST00000315491.12	NP_006077.2
TUBB3	NM_001197181.2	c.569G>A	p.Arg190His	missense_variant	Exon 4 of 4		NP_001184110.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TUBB3	ENST00000315491.12	c.785G>A	p.Arg262His	missense_variant	Exon 4 of 4	1	NM_006086.4	ENSP00000320295.7
ENSG00000198211	ENST00000556922.1	c.1826G>A	p.Arg609His	missense_variant	Exon 5 of 5	2		ENSP00000451560.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Nov 11, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 262 of the TUBB3 protein (p.Arg262His). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of congenital fibrosis of the extraocular muscles (PMID: 20074521, 24612975, 34652576). ClinVar contains an entry for this variant (Variation ID: 219256). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt TUBB3 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects TUBB3 function (PMID: 20074521, 26775887, 27046833). This variant disrupts the p.Arg262 amino acid residue in TUBB3. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 20074521, 29453417). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 29, 2015

Clinical Genetics and Genomics, Karolinska University Hospital

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Apr 16, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Published in vitro functional studies demonstrate that the presence of the R262H variant causes reduced binding of kinesin and non-motor proteins and exhibits altered polymerization dynamics (Minoura et al., 2016).; Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 27046833, 20074521, 27428177, 28840640, 31226147, 26582918, 26775887, 34652576, 27535533) -

Fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement Pathogenic:3 Other:1

Sep 27, 2019

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. -

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Aug 16, 2023

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is not observed in the gnomAD v2.1.1 dataset. Predicted Consequence/Location: Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product [REVEL: 0.87 (>=0.6, sensitivity 0.68 and specificity 0.92); 3Cnet: 0.95 (>=0.6, sensitivity 0.72 and precision 0.9)]. Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000219256 /PMID: 20074521). The variant has been previously reported as de novo in a similarly affected individual (PMID: 20074521), and observed in at least two similarly affected unrelated individuals (PMID: 20074521). A different missense change at the same codon (p.Arg262Cys) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000006963 /PMID: 20074521). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

Jan 01, 2015

Equipe Genetique des Anomalies du Developpement, Université de Bourgogne

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

TUBB3-related tubulinopathy Pathogenic:1

May 01, 2019

Illumina Laboratory Services, Illumina

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The TUBB3 c.785G>A (p.Arg262His) variant is a missense variant that has been reported in two studies, in which it is found in a de novo heterozygous state in three individuals with a severe form of congenital fibrosis of the extraocular muscles (CFEOM). Another variant at the same amino acid position has also been reported in 11 families with a milder form of CFEOM (Tischfield et al. 2010; MacKinnon et al. 2014). The p.Arg262His variant was absent from 1700 control chromosomes and is not found in the Genome Aggregation Database in a region of good sequence coverage, so the variant is presumed to be rare. Functional studies in yeast demonstrate that compared to wild-type microtubules, the p.Arg262His microtubules have prolonged growth events, longer astral microtubules, and an altered rate of polymerization and depolymerization. In vivo assays further demonstrate that p.Arg262His leads to significantly reduced kinesin interaction on microtubules and modifies the microtubule dynamics at both filament ends (Tischfield et al. 2010; Ti et al. 2016; Minoura et al. 2016). In vitro and in vivo transfection of variant TUBB3 resulted in reduced axon growth; this phenotype was rescued by co-transfection of a modified kinesin (Minoura et al. 2016). The p.Arg262His variant is predicted to abolish the hydrogen bond of the H8-S7 loop of b-tubulin and affect the tertiary protein structure and motor protein interactions with microtubules (Tischfield et al. 2010). Based on the collective evidence and application of the ACMG criteria, the p.Arg262His variant is classified as pathogenic for TUBB3-related tubulinopathy. -

TUBB3-related disorder Pathogenic:1

-

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been previously reported as a heterozygous change in patients with congenital fibrosis of extraocular muscles (CFEOM; PMID: 20074521, 34652576). A different amino acid change at the same residue (p.Arg262Cys) has been previously reported in individuals with CFEOM (PMID: 200774521, 27428177, 28832562, 29453417). Functional studies demonstrated that the c.785G>A (p.Arg262His) variant impairs both the motility and ATPase activity of kinesin and microtubule dynamics, which is required for normal axonal growth and brain development (PMID: 26775887, 27046833, 31226147). The c.785G>A (p.Arg262His) variant is absent from the gnomAD population database and thus is presumed to be rare. The c.785G>A (p.Arg262His) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, the c.785G>A (p.Arg262His) variant is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.39
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.93	.;.;D
Eigen	Pathogenic	0.77
Eigen_PC	Pathogenic	0.69
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.90	D;D;D
M_CAP	Pathogenic	0.83	D
MetaRNN	Pathogenic	0.99	D;D;D
MetaSVM	Pathogenic	0.90	D
MutationAssessor	Pathogenic	4.5	.;.;H
PrimateAI	Pathogenic	0.87	D
PROVEAN	Uncertain	-4.4	D;D;D
REVEL	Pathogenic	0.87
Sift	Uncertain	0.0090	D;.;.
Sift4G	Uncertain	0.015	D;D;D
Polyphen		0.93	.;.;P
Vest4		0.94
MutPred		0.98		.;.;Loss of methylation at R262 (P = 0.0249);
MVP		0.99
MPC		2.1
ClinPred		1.0	D
GERP RS		4.8
Varity_R		0.79
gMVP		0.98

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

Other links and lift over

dbSNP: rs864321716; hg19: chr16-90001644;