TTC39C

tetratricopeptide repeat domain 39C, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 18:23992773-24135970

Previous symbols: [ "C18orf17" ]

Links

ENSG00000168234 ∙ NCBI:125488 ∙ ∙ HGNC:26595 ∙ Uniprot:Q8N584 ∙ 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 TTC39C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC39C 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			29			29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	0	0

Variants in TTC39C

This is a list of pathogenic ClinVar variants found in the TTC39C region.

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

Position	Type	Phenotype	Significance	ClinVar
18-24014882-C-T		not specified	Uncertain significance (Apr 13, 2023)
18-24014906-G-A		not specified	Uncertain significance (Apr 25, 2023)
18-24014984-A-G		not specified	Uncertain significance (Aug 11, 2024)
18-24014986-A-G		not specified	Uncertain significance (Feb 16, 2023)
18-24069178-C-G		not specified	Uncertain significance (Oct 18, 2021)
18-24069188-T-C		not specified	Uncertain significance (Aug 15, 2024)
18-24080659-C-A		not specified	Uncertain significance (Sep 01, 2021)
18-24080707-G-C		not specified	Uncertain significance (Jun 21, 2023)
18-24080741-G-T		not specified	Uncertain significance (May 02, 2024)
18-24080743-G-T		not specified	Uncertain significance (Feb 07, 2023)
18-24080812-A-G		not specified	Uncertain significance (Nov 27, 2023)
18-24080819-T-C		not specified	Uncertain significance (Apr 08, 2022)
18-24080845-A-G		not specified	Uncertain significance (Nov 23, 2022)
18-24080873-G-A		not specified	Uncertain significance (Dec 27, 2022)
18-24080920-A-C		not specified	Uncertain significance (Jul 16, 2024)
18-24082952-T-G		not specified	Uncertain significance (Sep 03, 2024)
18-24082984-G-A		not specified	Uncertain significance (Dec 18, 2023)
18-24082990-A-T		not specified	Uncertain significance (Mar 14, 2023)
18-24083013-A-G		not specified	Uncertain significance (Jun 07, 2024)
18-24083069-A-G		not specified	Uncertain significance (Jul 19, 2022)
18-24114557-C-G		not specified	Uncertain significance (Sep 12, 2023)
18-24114558-A-G		not specified	Uncertain significance (Dec 15, 2023)
18-24114587-A-T		not specified	Uncertain significance (Nov 21, 2024)
18-24118138-G-A		not specified	Uncertain significance (Nov 08, 2022)
18-24118154-A-G		not specified	Uncertain significance (Oct 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC39C	protein_coding	protein_coding	ENST00000317571	14	142838

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000436	1.00	125720	0	26	125746	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.43	226	295	0.766	0.0000147	3822
Missense in Polyphen		55	87.315	0.62991		1122
Synonymous	0.611	103	111	0.926	0.00000565	1092
Loss of Function	3.47	12	33.8	0.355	0.00000197	393

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000701	0.0000701
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000114	0.000109
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000117	0.000114
Middle Eastern	0.000114	0.000109
South Asian	0.000131	0.000131
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.866
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.164
• hipred: Y
• hipred_score: 0.575
• ghis: 0.589

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.397

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc39c

Zebrafish Information Network

• Gene name: ttc39c
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology