rs267607164

chr16-89935700-G-Achr16-89935700-G-C

Variant summary

Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5_Very_Strong

The NM_006086.4(TUBB3):c.1249G>A(p.Asp417Asn) 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D417H) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: TUBB3 NM_006086.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:3 O:1
• Conservation: PhyloP100: 9.92

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]

ACMG classification

Verdict is Pathogenic. Variant got 17 ACMG points.

• PM1: In a helix (size 22) in uniprot entity TBB3_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_006086.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr16-89935700-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 6965.Status of the report is no_assertion_criteria_provided, 0 stars.
• PP2: Missense variant where missense usually causes diseases, TUBB3
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.922
• PP5: Variant 16-89935700-G-A is Pathogenic according to our data. Variant chr16-89935700-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 6966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TUBB3	NM_006086.4	c.1249G>A	p.Asp417Asn	missense_variant	4/4	ENST00000315491.12
TUBB3	NM_001197181.2	c.1033G>A	p.Asp345Asn	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TUBB3	ENST00000315491.12	c.1249G>A	p.Asp417Asn	missense_variant	4/4	1	NM_006086.4	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 08, 2010	- -
not provided, no classification provided	literature only	GeneReviews	-	- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Jul 03, 2021

This sequence change replaces aspartic acid with asparagine at codon 417 of the TUBB3 protein (p.Asp417Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with axonal peripheral neuropathy and/or congenital fibrosis of the extraocular muscles (PMID: 24257358, 25482575). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 6966). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C15"). For these reasons, this variant has been classified as Pathogenic. -

TUBB3-related tubulinopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

curation

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Mar 12, 2024

The heterozygous p.Asp417Asn variant in TUBB3 was identified by our study in one individual with congenital fibrosis of the extraocular muscles. This variant is assumed de novo in the individual, but maternity and paternity have not been confirmed. The p.Asp417Asn variant in TUBB3 has been previously reported in at least 7 unrelated individuals with congenital fibrosis of extraocular muscles 3A with or without extraocular involvement (PMID: 24257358, PMID: 25482575, PMID: 20074521, PMID: 34418069) and segregated with disease in 17 affected relatives from 4 families (PMID: 24257358, PMID: 25482575, PMID: 20074521). The number of reported affected individuals with this variant is greater than expected compared to non-affected individuals with this variant. This variant was found to be de novo in one individual with confirmed paternity and maternity (PMID: 20074521). This variant has also been reported in ClinVar (Variation ID: 6966) and has been interpreted as pathogenic by Invitae and OMIM. This variant was absent from large population studies. The number of missense variants reported in TUBB3 in the general population is lower than expected, suggesting there is little benign variation in this gene and slightly increasing the possibility that a missense variant in this gene may not be tolerated. The p.Asp417 variant is located in a region of TUBB3 that is essential to interactions with other motor proteins, suggesting that this variant is in a functional domain and slightly supports pathogenicity (PMID: 20074521). One additional likely pathogenic variant, resulting in a different amino acid change at the same position, p.Asp417His, has been reported in association with disease in the literature and in ClinVar, slightly supporting that a change at this position may not be tolerated (PMID: 20301522, Variation ID: 6965). In vitro functional studies provide some evidence that the p.Asp417Asn variant may impact protein function (PMID:31226147, PMID: 29382549). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, this variant meets criteria to be classified as pathogenic for autosomal dominant congenital fibrosis of extraocular muscles 3A with or without extraocular involvement. ACMG/AMP Criteria applied: PS2_Supporting, PS3_Supporting, PS4, PM1_Supporting, PM2_Supporting, PM5_Supporting, PM6_Supporting, PP1_Strong (Richards 2015). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Benign	-0.066	T
BayesDel_noAF	Benign	-0.33
Cadd	Pathogenic	33
Dann	Uncertain	1.0
Eigen	Pathogenic	0.83
Eigen_PC	Pathogenic	0.77
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.90	D;D;D
M_CAP	Uncertain	0.24	D
MetaRNN	Pathogenic	0.92	D;D;D
MetaSVM	Uncertain	0.25	D
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Pathogenic	0.87	D
PROVEAN	Uncertain	-3.0	D;N;N
REVEL	Uncertain	0.47
Sift	Uncertain	0.0010	D;.;.
Sift4G	Uncertain	0.016	D;D;D
Polyphen		1.0	.;.;D
Vest4		0.86
MutPred		0.81		.;.;Loss of phosphorylation at S420 (P = 0.1618);
MVP		0.93
MPC		2.6
ClinPred		0.97	D
GERP RS		4.7
Varity_R		0.60
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: rs267607164; hg19: chr16-90002108; COSMIC: COSV59248456; COSMIC: COSV59248456;