TTC9C

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

Basic information

Region (hg38): 11:62728069-62740293

Links

ENSG00000162222 ∙ NCBI:283237 ∙ ∙ HGNC:28432 ∙ Uniprot:Q8N5M4 ∙ 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 TTC9C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC9C 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in TTC9C

This is a list of pathogenic ClinVar variants found in the TTC9C region.

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

Position	Type	Phenotype	Significance	ClinVar
11-62728880-A-T		not specified	Uncertain significance (Jan 23, 2024)
11-62728906-C-T		not specified	Uncertain significance (Oct 14, 2021)
11-62728918-T-C		not specified	Uncertain significance (Aug 09, 2021)
11-62728935-T-A		not specified	Uncertain significance (Jan 21, 2025)
11-62728949-C-T		not specified	Uncertain significance (Jan 31, 2022)
11-62728990-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-62729013-G-C		not specified	Uncertain significance (Mar 31, 2022)
11-62729037-A-T		not specified	Uncertain significance (May 17, 2023)
11-62729072-A-G		not specified	Uncertain significance (Dec 19, 2023)
11-62735451-G-A		not specified	Uncertain significance (Feb 08, 2025)
11-62735472-C-A		not specified	Uncertain significance (Feb 06, 2024)
11-62735492-G-T		not specified	Uncertain significance (Apr 11, 2023)
11-62735526-G-A		not specified	Uncertain significance (Dec 18, 2023)
11-62738302-C-T		not specified	Uncertain significance (Dec 14, 2022)
11-62738342-A-G		not specified	Uncertain significance (Nov 07, 2022)
11-62738369-G-C		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC9C	protein_coding	protein_coding	ENST00000316461	3	12225

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000176	0.714	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.799	120	97.8	1.23	0.00000553	1093
Missense in Polyphen		34	25.842	1.3157		296
Synonymous	-0.180	42	40.5	1.04	0.00000214	342
Loss of Function	0.930	7	10.2	0.686	6.42e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000384	0.000384
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000123
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase (Consensus)

Intolerance Scores

• loftool: 0.571
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.110
• hipred: N
• hipred_score: 0.282
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.351

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc9c

Zebrafish Information Network

• Gene name: ttc9c
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Molecular function: protein binding