19-6495736-C-T

Position:

• chr19-6495736-C-T

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PP2 PP3_Moderate PP5

The ENST00000264071.7(TUBB4A):​c.763G>A​(p.Val255Ile) 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 Conflicting classifications of pathogenicity (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: TUBB4A ENST00000264071.7 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:9 U:1 O:1
• Conservation: PhyloP100: 7.69

Genes affected

TUBB4A (HGNC:20774): (tubulin beta 4A class IVa) This gene encodes a member of the beta tubulin family. Beta tubulins are one of two core protein families (alpha and beta tubulins) that heterodimerize and assemble to form microtubules. Mutations in this gene cause hypomyelinating leukodystrophy-6 and autosomal dominant torsion dystonia-4. Alternate splicing results in multiple transcript variants encoding different isoforms. A pseudogene of this gene is found on chromosome X. [provided by RefSeq, Jan 2014]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 3 uncertain in ENST00000264071.7
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), TUBB4A. . Gene score misZ 4.2623 (greater than the threshold 3.09). Trascript score misZ 5.1229 (greater than threshold 3.09). GenCC has associacion of gene with torsion dystonia 4, TUBB4A-related neurologic disorder, hypomyelinating leukodystrophy 6.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.909
• PP5: Variant 19-6495736-C-T is Pathogenic according to our data. Variant chr19-6495736-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 217025.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=2, Pathogenic=5, Uncertain_significance=1, not_provided=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TUBB4A	NM_006087.4	c.763G>A	p.Val255Ile	missense_variant	4/4	ENST00000264071.7	NP_006078.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TUBB4A	ENST00000264071.7	c.763G>A	p.Val255Ile	missense_variant	4/4	1	NM_006087.4	ENSP00000264071	P1
TUBB4A	ENST00000594276.5	c.451G>A	p.Val151Ile	missense_variant	3/3	4		ENSP00000472481

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:9 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Hypomyelinating leukodystrophy 6 Pathogenic:3 Uncertain:1 Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Mar 26, 2024	- -
Pathogenic, criteria provided, single submitter	research	TIDEX, University of British Columbia	-	- -
not provided, no classification provided	literature only	GeneReviews	-	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	UCLA Clinical Genomics Center, UCLA	Apr 02, 2013	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 04, 2023	This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 255 of the TUBB4A protein (p.Val255Ile). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with dystonia, isolated hypomyelination, or dystonia with hypomyelinating leukodystrophy (PMID: 25085639, 25326637; Invitae). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 217025). 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) performed at Invitae indicates that this missense variant is expected to disrupt TUBB4A protein function. Experimental studies have shown that this missense change affects TUBB4A function (PMID: 28973395). For these reasons, this variant has been classified as Pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 18, 2021	Published functional studies demonstrate a damaging effect with significant reduction in tubulin polymerization and altered ability to incorporate into microtubules, suggestive of a toxic dominant gain-of-function mechanism (Curiel et al, 2017); Not observed in large population cohorts (Lek et al., 2016); Missense variants in this gene are often considered pathogenic (Stenson et al., 2014); This variant is associated with the following publications: (PMID: 26934450, 25326637, 25085639, 27809427, 28973395, 32581362, 30542205) -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Jun 17, 2021	- -

Torsion dystonia 4 Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Oct 04, 2024

PS3,PS4,PM6,PM2 -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jun 04, 2021

The c.763G>A (p.V255I) alteration is located in exon 4 (coding exon 4) of the TUBB4A gene. This alteration results from a G to A substitution at nucleotide position 763, causing the valine (V) at amino acid position 255 to be replaced by an isoleucine (I). Based on data from the Genome Aggregation Database (gnomAD), the TUBB4A c.763G>A alteration was not observed, with coverage at this position. This alteration was reported de novo in a 5 year old girl with spastic quadriparesis, hypotonia, ataxia, developmental delay, and a brain MRI showing hypomyelination and mild cerebellar vermis atrophy (Pizzino, 2014). This alteration was reported de novo in another patient with developmental delay, microcephaly, truncal hypotonia, limb hypertonia, foot clonus, and cerebellar hypoplasia/atrophy (Lee, 2014). 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). Histo-pathological examination of brain tissue from affected individuals with the p.V255I alteration showed abnormal morphology of oligodendrocytes, and in vitro functional studies showed decreased tubulin polymerization and decreased myelin protein expression (Curiel, 2017). The p.V255I alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, this alteration is classified as likely pathogenic. -

Microcephaly Pathogenic:1

Pathogenic, criteria provided, single submitter

research

Bicknell laboratory, University of Otago

-

- -

Cerebral palsy Pathogenic:1

Likely pathogenic, no assertion criteria provided

research

NIHR Bioresource Rare Diseases, University of Cambridge

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.74
BayesDel_addAF	Uncertain	0.083	D
BayesDel_noAF	Benign	-0.12
CADD	Pathogenic	27
DANN	Uncertain	0.99
DEOGEN2	Benign	0.059	T;.
Eigen	Uncertain	0.62
Eigen_PC	Uncertain	0.54
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Benign	0.77	T;T
M_CAP	Pathogenic	0.93	D
MetaRNN	Pathogenic	0.91	D;D
MetaSVM	Uncertain	0.70	D
MutationAssessor	Pathogenic	3.3	M;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Pathogenic	0.80	T
PROVEAN	Benign	-0.85	N;.
REVEL	Pathogenic	0.88
Sift4G	Uncertain	0.024	D;D
Polyphen		0.92	P;.
Vest4		0.80
MutPred		0.74		Gain of ubiquitination at K252 (P = 0.0846);.;
MVP		0.87
MPC		2.5
ClinPred		0.99	D
GERP RS		4.0
Varity_R		0.74
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

Other links and lift over

dbSNP: rs767399782; hg19: chr19-6495747; COSMIC: COSV51158580; COSMIC: COSV51158580;