TTC22

tetratricopeptide repeat domain 22, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 1:54779712-54801323

Links

ENSG00000006555 ∙ NCBI:55001 ∙ ∙ HGNC:26067 ∙ Uniprot:Q5TAA0 ∙ 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 TTC22 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC22 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			28	3		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	4	0

Variants in TTC22

This is a list of pathogenic ClinVar variants found in the TTC22 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-54781281-C-T		not specified	Uncertain significance (Oct 05, 2021)
1-54781302-T-C		not specified	Uncertain significance (Nov 09, 2021)
1-54781482-C-G		not specified	Uncertain significance (Oct 14, 2021)
1-54781536-C-T		not specified	Uncertain significance (Apr 12, 2024)
1-54782329-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-54785555-G-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
1-54786026-C-T		not specified	Likely benign (Aug 01, 2022)
1-54786066-T-C		not specified	Uncertain significance (Jun 28, 2023)
1-54786077-C-T		not specified	Uncertain significance (Mar 28, 2023)
1-54786092-A-T		not specified	Uncertain significance (Aug 05, 2024)
1-54786104-C-T		not specified	Uncertain significance (Jun 16, 2023)
1-54787064-A-G		not specified	Uncertain significance (Apr 20, 2024)
1-54787719-C-T		not specified	Likely benign (May 23, 2023)
1-54787721-G-A			Likely benign (Feb 01, 2023)
1-54787722-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-54787747-G-A		not specified	Uncertain significance (Feb 28, 2023)
1-54787800-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-54787801-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-54800658-C-T		not specified	Uncertain significance (Jul 12, 2022)
1-54800659-G-C		not specified	Uncertain significance (Apr 04, 2023)
1-54800670-C-T		not specified	Uncertain significance (Aug 05, 2024)
1-54800704-C-G		not specified	Uncertain significance (Dec 12, 2024)
1-54800734-G-A		not specified	Uncertain significance (Mar 06, 2023)
1-54800734-G-C		not specified	Uncertain significance (Oct 27, 2021)
1-54800824-C-T		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC22	protein_coding	protein_coding	ENST00000371276	7	21556

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000171	0.876	125629	0	117	125746	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	239	292	0.819	0.0000177	3550
Missense in Polyphen		62	70.443	0.88015		922
Synonymous	2.17	100	132	0.760	0.00000868	1164
Loss of Function	1.54	12	19.3	0.621	0.00000101	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000460	0.000447
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.000336	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.000336	0.000326
South Asian	0.00269	0.00268
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Haploinsufficiency Scores

• pHI: 0.199
• hipred: N
• hipred_score: 0.238
• ghis: 0.425

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.694

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc22