TTC9

tetratricopeptide repeat domain 9, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 14:70641915-70675366

Links

ENSG00000133985 ∙ NCBI:23508 ∙ OMIM:610488 ∙ HGNC:20267 ∙ Uniprot:Q92623 ∙ 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 TTC9 gene.

• Inborn genetic diseases (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC9 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						0
missense			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in TTC9

This is a list of pathogenic ClinVar variants found in the TTC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-70642146-C-T		not specified	Uncertain significance (Sep 14, 2023)
14-70642152-C-G		not specified	Uncertain significance (May 27, 2022)
14-70642251-G-A		not specified	Uncertain significance (Jun 29, 2023)
14-70642322-G-A		not specified	Uncertain significance (Jun 05, 2023)
14-70642413-G-C		not specified	Uncertain significance (Dec 18, 2023)
14-70642437-C-T		not specified	Uncertain significance (Dec 12, 2023)
14-70642458-T-C		not specified	Likely benign (Sep 27, 2021)
14-70642481-G-A		not specified	Uncertain significance (Aug 11, 2022)
14-70667638-G-C		not specified	Uncertain significance (Jul 13, 2021)
14-70667707-C-T		not specified	Uncertain significance (Nov 13, 2023)
14-70671082-A-G		not specified	Uncertain significance (Jul 05, 2022)
14-70671111-A-T		not specified	Uncertain significance (Oct 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC9	protein_coding	protein_coding	ENST00000256367	3	33574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0682	0.877	124626	0	3	124629	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.489	80	93.3	0.858	0.00000473	1375
Missense in Polyphen		24	41.29	0.58125		501
Synonymous	0.592	36	40.8	0.882	0.00000206	460
Loss of Function	1.63	3	7.95	0.377	4.45e-7	108

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000177
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Haploinsufficiency Scores

• pHI: 0.0818
• hipred: N
• hipred_score: 0.412

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.159

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc9
• Phenotype: endocrine/exocrine gland phenotype; hematopoietic system phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); immune system phenotype

Gene ontology

• Biological process: bone development