TRAK2

trafficking kinesin protein 2

Basic information

Region (hg38): 2:201377206-201451500

Previous symbols: [ "ALS2CR3" ]

Links

ENSG00000115993 ∙ NCBI:66008 ∙ OMIM:607334 ∙ HGNC:13206 ∙ Uniprot:O60296 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TRAK2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRAK2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			47	1		48
nonsense				1		1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding				1		1
Total	0	0	47	3	2

Variants in TRAK2

This is a list of pathogenic ClinVar variants found in the TRAK2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-201380549-C-G		not specified	Uncertain significance (Dec 01, 2022)
2-201380592-G-A		not specified	Uncertain significance (Dec 12, 2023)
2-201380613-A-C		not specified	Uncertain significance (Sep 14, 2022)
2-201380617-G-A		not specified	Uncertain significance (Mar 15, 2024)
2-201380676-G-A		not specified	Uncertain significance (Nov 09, 2022)
2-201380692-G-A			Likely benign (Nov 01, 2021)
2-201380751-A-T		not specified	Uncertain significance (Jan 26, 2022)
2-201380790-T-A		not specified	Uncertain significance (Aug 22, 2023)
2-201380869-G-T		not specified	Uncertain significance (Dec 03, 2021)
2-201380940-T-C		not specified	Uncertain significance (Jun 10, 2024)
2-201380973-G-A		not specified	Uncertain significance (Jan 09, 2024)
2-201381045-C-T		not specified	Uncertain significance (Jan 31, 2024)
2-201381165-G-C		not specified	Uncertain significance (Apr 29, 2024)
2-201381184-C-T		not specified	Uncertain significance (Dec 16, 2023)
2-201381221-TAAA-T			Benign (Jan 02, 2024)
2-201381232-A-AG			Likely benign (Jan 02, 2024)
2-201384127-T-G		not specified	Uncertain significance (Jul 19, 2022)
2-201384130-T-C		not specified	Uncertain significance (Mar 04, 2024)
2-201384211-T-G		not specified	Uncertain significance (Mar 27, 2023)
2-201386260-T-C		not specified	Uncertain significance (Sep 01, 2021)
2-201386318-C-G		not specified	Uncertain significance (Aug 17, 2021)
2-201386382-G-A		not specified	Uncertain significance (Jul 19, 2023)
2-201386394-A-C		not specified	Uncertain significance (Jan 16, 2024)
2-201386397-C-G		not specified	Uncertain significance (Jan 07, 2022)
2-201386399-T-G		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRAK2	protein_coding	protein_coding	ENST00000332624	15	74373

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.91e-14	0.986	125514	2	232	125748	0.000931

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.487	458	488	0.938	0.0000259	5941
Missense in Polyphen		163	183.47	0.88841		2231
Synonymous	0.434	171	178	0.959	0.00000896	1812
Loss of Function	2.56	30	49.4	0.607	0.00000314	537

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000744	0.000744
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.000381	0.000381
Finnish	0.00180	0.00180
European (Non-Finnish)	0.00126	0.00124
Middle Eastern	0.000381	0.000381
South Asian	0.000529	0.000523
Other	0.00114	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May regulate endosome-to-lysosome trafficking of membrane cargo, including EGFR. {ECO:0000250}.
• Pathway: GABAergic synapse - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.905
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.66

Haploinsufficiency Scores

• pHI: 0.698
• hipred: Y
• hipred_score: 0.560
• ghis: 0.501

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trak2

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;protein O-linked glycosylation;protein targeting;anterograde axonal transport;protein localization;endosome to lysosome transport;neurogenesis;vesicle transport along microtubule;mitochondrion distribution;dendrite morphogenesis;negative regulation of axonogenesis;anterograde axonal transport of mitochondrion;anterograde dendritic transport of mitochondrion
• Cellular component: nucleus;cytoplasm;mitochondrion;early endosome;plasma membrane;dendrite;cytoplasmic vesicle;dendrite cytoplasm;neuronal cell body;axonal growth cone;axon cytoplasm
• Molecular function: signaling receptor binding;protein binding;myosin binding;kinesin binding;enzyme binding;TPR domain binding;GABA receptor binding