rs267607164

Variant names:

• chr16-89935700-G-A
• rs267607164
• NM_006086.4:c.1249G>A

Your query was ambiguous. Multiple possible variants found:

• chr16-89935700-G-A
• chr16-89935700-G-C

Variant summary

Our verdict is Pathogenic. The variant received 15 ACMG points: 15P and 0B. 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:4 O:1
• Conservation: PhyloP100: 9.92
• Publications: 34 publications found

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]

TUBB3 Gene-Disease associations (from GenCC):

• complex cortical dysplasia with other brain malformations 1

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Illumina
• fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement

  Inheritance: AD Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
• congenital fibrosis of extraocular muscles

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• tubulinopathy-associated dysgyria

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ENSG00000198211 (HGNC:):

ACMG classification

Our verdict: Pathogenic. The variant received 15 ACMG points.

• 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 VariationId is 6965.Status of the report is no_assertion_criteria_provided, 0 stars.
• 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 fibrosis of extraocular muscles, congenital, 3A, with or without extraocular involvement, tubulinopathy-associated dysgyria, congenital fibrosis of extraocular muscles, complex cortical dysplasia with other brain malformations 1.
• 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 VariationId is 6966.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.1249G>A	p.Asp417Asn	missense_variant	Exon 4 of 4	ENST00000315491.12	NP_006077.2
TUBB3	NM_001197181.2	c.1033G>A	p.Asp345Asn	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.1249G>A	p.Asp417Asn	missense_variant	Exon 4 of 4	1	NM_006086.4	ENSP00000320295.7
ENSG00000198211	ENST00000556922.1	c.2290G>A	p.Asp764Asn	missense_variant	Exon 5 of 5	2		ENSP00000451560.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4 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

-

GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Jan 08, 2010

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

not provided Pathogenic:1

Jul 03, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

For these reasons, this variant has been classified as Pathogenic. 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"). 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). -

Complex cortical dysplasia with other brain malformations 1 Pathogenic:1

May 10, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: TUBB3 c.1249G>A (p.Asp417Asn) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 251228 control chromosomes. c.1249G>A has been reported in the literature in multiple individuals affected with Cortical Dysplasia, Complex, With Other Brain Malformations 1 (example, Tischfield_ 2010). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal funciton (Huang_2018, Tischfield_ 2010). The following publications have been ascertained in the context of this evaluation (PMID: 29382549, 20074521). ClinVar contains an entry for this variant (Variation ID: 6966). Based on the evidence outlined above, the variant was classified as pathogenic. -

TUBB3-related tubulinopathy Pathogenic:1

Mar 12, 2024

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

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
DEOGEN2	Uncertain	0.52	.;.;D
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
MutationAssessor	Benign	1.8	.;.;L
PhyloP100		9.9
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
Mutation Taster		=5/95	disease causing (ClinVar)

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

Other links and lift over

dbSNP: rs267607164; hg19: chr16-90002108; COSMIC: COSV59248456; COSMIC: COSV59248456;