TRANK1

tetratricopeptide repeat and ankyrin repeat containing 1, the group of Tetratricopeptide repeat domain containing|Ankyrin repeat domain containing

Basic information

Region (hg38): 3:36826819-36945057

Links

ENSG00000168016 ∙ NCBI:9881 ∙ OMIM:619316 ∙ HGNC:29011 ∙ Uniprot:O15050 ∙ 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 TRANK1 gene.

• not_specified (407 variants)
• not_provided (12 variants)
• Autism (2 variants)
• Autism_spectrum_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRANK1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001329998.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				10		10
missense			386	23		409
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2			2
Total	0	0	388	33	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRANK1	protein_coding	protein_coding	ENST00000429976	23	118238

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.01e-25	1.00	124539	1	133	124673	0.000538

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	1329	1.56e+3	0.852	0.0000895	19311
Missense in Polyphen		340	448.78	0.75762		5641
Synonymous	-0.350	627	616	1.02	0.0000357	5562
Loss of Function	4.48	59	110	0.538	0.00000584	1435

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00121	0.00121
Ashkenazi Jewish	0.00	0.00
East Asian	0.000114	0.000111
Finnish	0.000465	0.000464
European (Non-Finnish)	0.000700	0.000628
Middle Eastern	0.000114	0.000111
South Asian	0.000461	0.000425
Other	0.000518	0.000495

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -3.56
• rvis_percentile_EVS: 0.31

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.414
• ghis: 0.551

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trank1