TACC2

protein-coding

transforming acidic coiled-coil containing protein 2, the group of TACC family

Gene summary

Transforming acidic coiled-coil proteins are a conserved family of centrosome- and microtubule-interacting proteins that are implicated in cancer. This gene encodes a protein that concentrates at centrosomes throughout the cell cycle. This gene lies within a chromosomal region associated with tumorigenesis. Expression of this gene is induced by erythropoietin and is thought to affect the progression of breast tumors. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_206862.4

Inheritance

—

ClinVar variants

U:448B:75

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr10:121,989,163-122,254,545

External References & Databases

Ensembl (ENSG00000138162)

Transcript & Mutation Effects

hg38 • Region Span ~265.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TACC2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 476

not providedTotal: 30

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_206862.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	8 clinvar	2 clinvar	15
missense			439 clinvar	58 clinvar	7 clinvar	504
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	448	66	9	523

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 104 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_206862.4	RefSeq	NP_996744.4	22	MANE Select
ENST00000369005.6	Ensembl	ENSP00000358001.1	22	MANE Select
NM_001291876.2	RefSeq	NP_001278805.2	19	Standard
NM_001291877.2	RefSeq	NP_001278806.2	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization
mitotic spindle organization
cell population proliferation
cerebral cortex development

Molecular Function

nuclear hormone receptor binding

Cellular Component

nucleoplasm
cytoplasm
microtubule organizing center
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369005
Coding exons: 22
Length: 265372
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.390	1593	1.64e+3	0.973	0.0000910	18960
Missense (PolyPhen)		363	420.91	0.86242		5013
Synonymous	-2.12	765	694	1.10	0.0000458	6281
Loss of Function	4.21	55	101	0.547	0.00000512	1267

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in the microtubule-dependent coupling of the nucleus and the centrosome. Involved in the processes that regulate centrosome-mediated interkinetic nuclear migration (INM) of neural progenitors (By similarity). May play a role in organizing centrosomal microtubules. May act as a tumor suppressor protein. May represent a tumor progression marker. {ECO:0000250, ECO:0000269|PubMed:10749935}.;

Recessive Scores

pRec: 0.0831

Intolerance Scores

LoFtool: 0.843
RVIS EVS: 4.1
RVIS percentile EVS: 99.68

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.476

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	High	Medium	High
Cancer	High	High	High