TUBB4A (tubulin beta 4A class IVa)

Gene

• Entrez ID: 10382
• Gene name: Tubulin beta 4A class IVa
• Gene symbol: TUBB4A
• Synonyms (NCBI Gene): DYT4, TUBB4, beta-5
• Chromosome: 19
• Chromosome location: 19p13.3
• Summary: 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 au

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs369467354	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs483352809	C>T	Pathogenic	Coding sequence variant, missense variant
rs587776983	G>A,C,T	Pathogenic	5 prime UTR variant, coding sequence variant, synonymous variant, missense variant
rs587777074	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs587777428	C>T	Pathogenic	Coding sequence variant, missense variant
rs587777429	C>A,T	Pathogenic	Coding sequence variant, missense variant
rs587777467	C>G,T	Pathogenic	5 prime UTR variant, coding sequence variant, missense variant
rs587777468	G>A,C	Pathogenic	Coding sequence variant, missense variant
rs748787734	G>A,C	Likely-pathogenic	Synonymous variant, coding sequence variant, missense variant
rs756762431	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs761635539	G>A	Pathogenic	Missense variant, coding sequence variant
rs767399782	C>A,T	Pathogenic-likely-pathogenic, pathogenic, likely-pathogenic	Missense variant, coding sequence variant
rs797045074	C>G,T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs886039470	C>T	Pathogenic	Missense variant, coding sequence variant
rs886041007	C>G,T	Pathogenic	Missense variant, coding sequence variant
rs886041008	G>T	Pathogenic	Missense variant, coding sequence variant
rs886041009	C>A	Pathogenic	Missense variant, coding sequence variant
rs886041010	C>A,T	Pathogenic	Missense variant, coding sequence variant
rs886041011	G>T	Pathogenic	Missense variant, coding sequence variant
rs886041012	C>A	Pathogenic	Missense variant, coding sequence variant
rs886041013	G>A	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs886041014	A>C	Pathogenic	Missense variant, coding sequence variant
rs886041015	C>A,T	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs886041016	C>T	Pathogenic	Missense variant, coding sequence variant
rs886041017	G>T	Pathogenic	Missense variant, coding sequence variant
rs886041018	A>G,T	Pathogenic	Missense variant, coding sequence variant
rs886041019	T>C	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs886041020	A>G	Pathogenic	Missense variant, coding sequence variant
rs886041021	C>A,T	Pathogenic	Missense variant, coding sequence variant
rs886041022	A>C,G	Likely-pathogenic, pathogenic	Missense variant, coding sequence variant
rs1057517986	C>G	Pathogenic	Coding sequence variant, missense variant
rs1131691696	C>T	Pathogenic-likely-pathogenic	Coding sequence variant, missense variant
rs1599405952	G>T	Likely-pathogenic	Coding sequence variant, missense variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT022751	hsa-miR-124-3p	Microarray	18668037
MIRT036536	hsa-miR-1226-3p	CLASH	23622248
MIRT513393	hsa-miR-3974	PAR-CLIP	23446348
MIRT513392	hsa-miR-488-5p	PAR-CLIP	23446348
MIRT513390	hsa-miR-150-5p	PAR-CLIP	23446348
MIRT513391	hsa-miR-532-3p	PAR-CLIP	23446348
MIRT513389	hsa-miR-2116-3p	PAR-CLIP	23446348
MIRT513388	hsa-miR-6845-3p	PAR-CLIP	23446348
MIRT513387	hsa-miR-1909-3p	PAR-CLIP	23446348
MIRT513386	hsa-miR-6722-3p	PAR-CLIP	23446348
MIRT513385	hsa-miR-1207-5p	PAR-CLIP	23446348
MIRT513384	hsa-miR-4763-3p	PAR-CLIP	23446348
MIRT513383	hsa-miR-4713-5p	PAR-CLIP	23446348
MIRT513381	hsa-miR-6873-3p	PAR-CLIP	23446348
MIRT513382	hsa-miR-4768-5p	PAR-CLIP	23446348
MIRT513380	hsa-miR-6833-3p	PAR-CLIP	23446348
MIRT513379	hsa-miR-6809-3p	PAR-CLIP	23446348
MIRT513393	hsa-miR-3974	PAR-CLIP	23446348
MIRT513392	hsa-miR-488-5p	PAR-CLIP	23446348
MIRT513390	hsa-miR-150-5p	PAR-CLIP	23446348
MIRT513391	hsa-miR-532-3p	PAR-CLIP	23446348
MIRT513389	hsa-miR-2116-3p	PAR-CLIP	23446348
MIRT513388	hsa-miR-6845-3p	PAR-CLIP	23446348
MIRT513387	hsa-miR-1909-3p	PAR-CLIP	23446348
MIRT513386	hsa-miR-6722-3p	PAR-CLIP	23446348
MIRT513385	hsa-miR-1207-5p	PAR-CLIP	23446348
MIRT513384	hsa-miR-4763-3p	PAR-CLIP	23446348
MIRT513383	hsa-miR-4713-5p	PAR-CLIP	23446348
MIRT513381	hsa-miR-6873-3p	PAR-CLIP	23446348
MIRT513382	hsa-miR-4768-5p	PAR-CLIP	23446348
MIRT513380	hsa-miR-6833-3p	PAR-CLIP	23446348
MIRT513379	hsa-miR-6809-3p	PAR-CLIP	23446348

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000226	Process	Microtubule cytoskeleton organization	IBA
GO:0000278	Process	Mitotic cell cycle	IBA
GO:0003924	Function	GTPase activity	IEA
GO:0005200	Function	Structural constituent of cytoskeleton	IBA
GO:0005200	Function	Structural constituent of cytoskeleton	IEA
GO:0005509	Function	Calcium ion binding	IMP	10211825
GO:0005515	Function	Protein binding	IPI	20195357, 24275654, 31046837
GO:0005525	Function	GTP binding	IBA
GO:0005525	Function	GTP binding	IEA
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005874	Component	Microtubule	IBA
GO:0005874	Component	Microtubule	IDA	21525035
GO:0005874	Component	Microtubule	IEA
GO:0005929	Component	Cilium	IEA
GO:0005930	Component	Axoneme	IDA	12475942
GO:0007017	Process	Microtubule-based process	IEA
GO:0015630	Component	Microtubule cytoskeleton	IDA
GO:0031115	Process	Negative regulation of microtubule polymerization	IMP	10211825
GO:0033269	Component	Internode region of axon	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043025	Component	Neuronal cell body	IEA
GO:0043209	Component	Myelin sheath	IEA
GO:0045171	Component	Intercellular bridge	IDA
GO:0045171	Component	Intercellular bridge	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	23533145
GO:0072686	Component	Mitotic spindle	IDA
GO:0072686	Component	Mitotic spindle	IEA

Other IDs

• MIM: 602662
• HGNC: 20774
• e!Ensembl: ENSG00000104833

Protein

• UniProt ID: P04350
• Protein name: Tubulin beta-4A chain (Tubulin 5 beta) (Tubulin beta-4 chain)
• Protein function: Tubulin is the major constituent of microtubules, a cylinder consisting of laterally associated linear protofilaments composed of alpha- and beta-tubulin heterodimers. Microtubules grow by the addition of GTP-tubulin dimers to the microtubule en
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00091	Tubulin	3 → 212	Tubulin/FtsZ family, GTPase domain	Domain
  PF03953	Tubulin_C	261 → 383	Tubulin C-terminal domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Major isotype in brain, where it represents 46% of all beta-tubulins. In the brain, highest expression levels in the cerebellum, followed by putamen and white matter. Moderate levels in testis. Very low levels, if any, in other tissues
• Sequence:

  MREIVHLQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLERINVYYNEATGGNYV
  PRAVLVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDAVLDVV
  RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEFPDRIMNTFSVVPSPKVSDTVV
  EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
  RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
  AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLSVQSKNSSYFVEWIPNNVKTAVCDIPPRG
  LKMAATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
  EYQQYQDATAEEGEFEEEAEEEVA

• Sequence length: 444

Pathways

KEGG:

Phagosome
Gap junction
Motor proteins
Alzheimer disease
Parkinson disease
Amyotrophic lateral sclerosis
Huntington disease
Prion disease
Pathways of neurodegeneration - multiple diseases
Pathogenic Escherichia coli infection
Salmonella infection

Reactome:

Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane
MHC class II antigen presentation
Separation of Sister Chromatids
Resolution of Sister Chromatid Cohesion
Regulation of PLK1 Activity at G2/M Transition
HSP90 chaperone cycle for steroid hormone receptors (SHR)
Loss of Nlp from mitotic centrosomes
Recruitment of mitotic centrosome proteins and complexes
Loss of proteins required for interphase microtubule organization from the centrosome
Recruitment of NuMA to mitotic centrosomes
Recycling pathway of L1
Hedgehog 'off' state
Cilium Assembly
Anchoring of the basal body to the plasma membrane
Intraflagellar transport
RHO GTPases activate IQGAPs
RHO GTPases Activate Formins
COPI-mediated anterograde transport
COPI-dependent Golgi-to-ER retrograde traffic
COPI-independent Golgi-to-ER retrograde traffic
Mitotic Prometaphase
The role of GTSE1 in G2/M progression after G2 checkpoint
AURKA Activation by TPX2
Carboxyterminal post-translational modifications of tubulin
HCMV Early Events
Aggrephagy
EML4 and NUDC in mitotic spindle formation
Sealing of the nuclear envelope (NE) by ESCRT-III
Kinesins

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Abnormality of the nervous system	Likely pathogenic; Pathogenic	rs483352809	RCV001814029	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Auditory neuropathy spectrum disorder	Likely pathogenic; Pathogenic	rs886039470	RCV003984834	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Cerebral palsy	Likely pathogenic; Pathogenic	rs587777428, rs767399782	RCV001795219 RCV001004001	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic; Pathogenic	rs587777428	RCV002463648	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypomyelinating leukodystrophy 6	Likely pathogenic; Pathogenic	rs2145244590, rs587777428, rs587777429, rs2145244734, rs587777467, rs587777468, rs886041008, rs2512754593, rs761635539, rs797045074, rs767399782, rs2512753619, rs1914525410, rs886039470, rs886041021, rs886041019, rs886041018, rs886041013, rs886041011, rs886041010, rs886041007, rs587776983, rs2512753517, rs1131691696, rs748787734, rs1568409626, rs483352809, rs886041022, rs1599405952, rs886041015, rs1914104455	RCV001663402 RCV000122736 RCV000122737 RCV002014654 RCV000128409 RCV000128410 RCV002262174 RCV002471533 RCV000173012 RCV000191139 RCV000199587 RCV003057342 RCV003148341 RCV000258674 RCV000258636 RCV000258534 RCV000258588 RCV000258517 RCV000258759 RCV000258678 RCV000258532 RCV000258787 RCV000258699 RCV000258578 RCV003742076 RCV001851359 RCV000552933 RCV000704674 RCV000258667 RCV000043681 RCV000850614 RCV000990137 RCV000995672 RCV000995673 RCV001195857	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Leukodystrophy	Likely pathogenic; Pathogenic	rs886041007	RCV005625493	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Microcephaly	Likely pathogenic; Pathogenic	rs767399782	RCV001527369	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Torsion dystonia 4	Likely pathogenic; Pathogenic	rs552079378, rs587777428, rs886041008, rs767399782, rs886041021, rs587777468, rs1131691696, rs587776983, rs483352809, rs886041022	RCV001335377 RCV000763442 RCV002262174 RCV004798804 RCV001249222 RCV001335376 RCV003458202 RCV000043680 RCV001249621 RCV000850614	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
TUBB4A-related disorder	Likely pathogenic; Pathogenic	rs587777429	RCV003982897	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
TUBB4A-related neurologic disorder	Likely pathogenic; Pathogenic	rs886041021	RCV006249623	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ATROPHY/DEGENERATION AFFECTING THE CEREBELLUM	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Brown syndrome	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BROWN TENDON SHEATH SYNDROME	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Classic medulloblastoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CONGENITAL NEUROLOGIC ANOMALIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA 4, TORSION, AUTOSOMAL DOMINANT	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA MUSCULORUM DEFORMANS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DYSTONIA MUSCULORUM DEFORMANS 4	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dystonic disorder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FAMILIAL TORSION DYSTONIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
FRONTOTEMPORAL DEMENTIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GENETIC TORSION DYSTONIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
IDIOPATHIC FAMILIAL DYSTONIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEUKODYSTROPHY, HYPOMYELINATING, 6	—	Disgenet, HPO Disgenet, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRIMARY DYSTONIA, DYT4 TYPE	—	Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TUBB4A-related hypomyelinating leukodystrophy and/or torsion dystonia	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
WHISPERING DYSPHONIA, HEREDITARY	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Relationship Type	References	Evidence Score
Anodontia	Associate	23582646, 28655586, 28973395, 35275727, 37003180	★☆☆☆☆ Found in Text Mining only
Atrophy	Associate	34514881	★☆☆☆☆ Found in Text Mining only
Basal Ganglia Diseases	Associate	24785942	★☆☆☆☆ Found in Text Mining only
Brain Diseases	Associate	28973395	★☆☆☆☆ Found in Text Mining only
Cerebellar Diseases	Associate	25085639	★☆☆☆☆ Found in Text Mining only
Chorea	Associate	24598712	★☆☆☆☆ Found in Text Mining only
Ciliary Dyskinesia With Transposition Of Ciliary Microtubules	Associate	28973395	★☆☆☆☆ Found in Text Mining only
Congenital Hereditary and Neonatal Diseases and Abnormalities	Associate	34514881	★☆☆☆☆ Found in Text Mining only
Demyelinating Diseases	Associate	24742798, 24785942, 25085639, 28973395, 29451896, 34514881, 40179460	★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Associate	34514881	★☆☆☆☆ Found in Text Mining only
Dysphonia	Associate	23595291	★☆☆☆☆ Found in Text Mining only
Dystonia	Associate	23582646, 23595291, 24598712, 28655586, 32943487, 35275727	★☆☆☆☆ Found in Text Mining only
Dystonia musculorum deformans 4	Associate	24785942	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Dystonic Disorders	Associate	24598712, 24742798, 28655586, 28973395	★☆☆☆☆ Found in Text Mining only
Heredodegenerative Disorders Nervous System	Associate	24742798	★☆☆☆☆ Found in Text Mining only
Hypoxia Brain	Associate	31940282	★☆☆☆☆ Found in Text Mining only
Immunoglobulin G4 Related Disease	Associate	34997144	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Associate	24598712	★☆☆☆☆ Found in Text Mining only
Laryngitis	Associate	32943487	★☆☆☆☆ Found in Text Mining only
Leukodystrophy Hypomyelinating 6	Associate	23582646, 24598712, 24742798, 24785942, 25085639, 28655586, 28973395, 35275727, 37003180	★☆☆☆☆ Found in Text Mining only
Leukodystrophy Metachromatic	Associate	32573057, 37003180, 37461315	★☆☆☆☆ Found in Text Mining only
Leukoencephalopathies	Associate	24598712, 34514881, 35803560	★☆☆☆☆ Found in Text Mining only
Livedoid Vasculopathy	Associate	40179460	★☆☆☆☆ Found in Text Mining only
Melanoma Cutaneous Malignant	Associate	36173063	★☆☆☆☆ Found in Text Mining only
Mental Disorders	Associate	24598712	★☆☆☆☆ Found in Text Mining only
Movement Disorders	Associate	37461315	★☆☆☆☆ Found in Text Mining only
Neoplasm Metastasis	Associate	35589707	★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	15986332, 35589707	★☆☆☆☆ Found in Text Mining only
Nervous System Diseases	Associate	37461315	★☆☆☆☆ Found in Text Mining only
Neurologic Manifestations	Associate	28973395, 34514881	★☆☆☆☆ Found in Text Mining only
Pelizaeus Merzbacher like disease autosomal recessive 2	Associate	24742798, 28655586, 33597727	★☆☆☆☆ Found in Text Mining only
Personality Disorders	Stimulate	35589707	★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Stimulate	35589707	★☆☆☆☆ Found in Text Mining only
Psychomotor Disorders	Associate	40179460	★☆☆☆☆ Found in Text Mining only
Quadriplegia	Associate	28973395	★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Stimulate	37161060	★☆☆☆☆ Found in Text Mining only
Status Asthmaticus	Associate	29843677	★☆☆☆☆ Found in Text Mining only
Thakker Donnai syndrome	Associate	24598712	★☆☆☆☆ Found in Text Mining only
Torticollis	Associate	28655586, 32943487	★☆☆☆☆ Found in Text Mining only
Whispering dysphonia hereditary	Associate	23595291, 24598712, 28655586	★☆☆☆☆ Found in Text Mining only