TTC16

tetratricopeptide repeat domain 16, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 9:127716079-127731590

Links

ENSG00000167094 ∙ NCBI:158248 ∙ ∙ HGNC:26536 ∙ Uniprot:Q8NEE8 ∙ 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 TTC16 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC16 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				1		1
missense			63	8		71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	63	9	0

Variants in TTC16

This is a list of pathogenic ClinVar variants found in the TTC16 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-127716894-G-C		not specified	Uncertain significance (Jun 13, 2023)
9-127716926-A-C		not specified	Uncertain significance (Oct 06, 2021)
9-127716954-A-T		not specified	Uncertain significance (Mar 02, 2023)
9-127716955-A-T		not specified	Uncertain significance (Nov 09, 2021)
9-127716998-C-T		not specified	Uncertain significance (Dec 18, 2023)
9-127717401-G-A		not specified	Uncertain significance (Sep 13, 2022)
9-127717668-C-T		not specified	Uncertain significance (Jan 22, 2024)
9-127717690-C-T		not specified	Uncertain significance (Mar 18, 2024)
9-127717698-C-G		not specified	Uncertain significance (Jan 09, 2024)
9-127717702-G-A		Premature ovarian insufficiency	Uncertain significance (-)
9-127717715-A-G			Likely benign (May 01, 2022)
9-127720334-A-T		not specified	Uncertain significance (Nov 17, 2022)
9-127720337-A-G		not specified	Likely benign (Feb 16, 2023)
9-127720360-A-G		not specified	Uncertain significance (Nov 09, 2021)
9-127720364-T-C		not specified	Uncertain significance (Jan 23, 2024)
9-127720366-C-T		not specified	Uncertain significance (Nov 16, 2021)
9-127723222-C-T		not specified	Uncertain significance (Jun 11, 2021)
9-127723225-G-A		not specified	Uncertain significance (Apr 05, 2023)
9-127723234-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-127723264-A-G		not specified	Uncertain significance (Feb 27, 2023)
9-127723276-A-G		not specified	Uncertain significance (Sep 27, 2021)
9-127723315-C-T		not specified	Uncertain significance (Nov 03, 2023)
9-127724137-G-A		not specified	Uncertain significance (Jul 21, 2021)
9-127724175-A-G		not specified	Uncertain significance (Jul 25, 2023)
9-127724224-C-T		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC16	protein_coding	protein_coding	ENST00000373289	14	15535

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.11e-18	0.0386	125401	0	343	125744	0.00136

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.431	477	504	0.946	0.0000297	5674
Missense in Polyphen		138	133.79	1.0315		1450
Synonymous	0.911	198	215	0.921	0.0000130	1705
Loss of Function	0.855	30	35.5	0.845	0.00000174	390

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00569	0.00567
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00368	0.00365
Finnish	0.0000482	0.0000462
European (Non-Finnish)	0.000613	0.000563
Middle Eastern	0.00368	0.00365
South Asian	0.00161	0.00157
Other	0.00101	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.980
• rvis_EVS: 0.65
• rvis_percentile_EVS: 84.18

Haploinsufficiency Scores

• pHI: 0.175
• hipred: N
• hipred_score: 0.153
• ghis: 0.417

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc16