TTC23L

tetratricopeptide repeat domain 23 like

Basic information

Region (hg38): 5:34838832-34900511

Links

ENSG00000205838 ∙ NCBI:153657 ∙ OMIM:616344 ∙ HGNC:26355 ∙ Uniprot:Q6PF05 ∙ 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 TTC23L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC23L 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in TTC23L

This is a list of pathogenic ClinVar variants found in the TTC23L region.

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

Position	Type	Phenotype	Significance	ClinVar
5-34840715-T-A		not specified	Uncertain significance (Jan 17, 2023)
5-34840722-G-C		not specified	Uncertain significance (Mar 01, 2023)
5-34845636-C-A		not specified	Uncertain significance (Aug 08, 2022)
5-34845636-C-T		not specified	Uncertain significance (Aug 30, 2021)
5-34845665-G-A		not specified	Uncertain significance (May 14, 2024)
5-34850216-G-A		not specified	Uncertain significance (Mar 01, 2023)
5-34850231-G-A		not specified	Uncertain significance (Jan 26, 2023)
5-34850270-C-T		not specified	Uncertain significance (May 31, 2023)
5-34850294-A-T		not specified	Uncertain significance (Feb 23, 2023)
5-34862915-A-G		not specified	Uncertain significance (Mar 28, 2023)
5-34864540-G-A		not specified	Uncertain significance (Sep 29, 2023)
5-34864553-C-G		not specified	Uncertain significance (Mar 18, 2024)
5-34866921-T-C		not specified	Uncertain significance (Feb 06, 2023)
5-34867005-A-G		not specified	Uncertain significance (Sep 01, 2021)
5-34867020-T-C		not specified	Uncertain significance (Jul 26, 2023)
5-34867021-A-G		not specified	Uncertain significance (Nov 17, 2023)
5-34867045-C-A		not specified	Uncertain significance (Jul 08, 2022)
5-34868905-G-T		not specified	Uncertain significance (Mar 01, 2023)
5-34868914-G-A		not specified	Likely benign (Oct 30, 2023)
5-34868933-C-T		not specified	Uncertain significance (Sep 17, 2021)
5-34868953-G-T		not specified	Uncertain significance (Dec 19, 2023)
5-34868966-C-A		not specified	Uncertain significance (Feb 03, 2022)
5-34868984-A-T		not specified	Uncertain significance (May 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC23L	protein_coding	protein_coding	ENST00000505624	9	60624

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.02e-11	0.205	124116	3	521	124640	0.00210

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.566	165	187	0.883	0.00000908	2343
Missense in Polyphen		46	48.053	0.95728		644
Synonymous	0.731	66	74.0	0.892	0.00000395	676
Loss of Function	0.745	18	21.8	0.828	0.00000115	257

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00227	0.00226
Ashkenazi Jewish	0.00447	0.00448
East Asian	0.00696	0.00698
Finnish	0.000418	0.000418
European (Non-Finnish)	0.000889	0.000885
Middle Eastern	0.00696	0.00698
South Asian	0.00600	0.00587
Other	0.00199	0.00198

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.831
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.56

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.152

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc23l

Gene ontology

• Biological process: response to endoplasmic reticulum stress
• Cellular component: cytoplasm;microtubule organizing center;spindle;midbody
• Molecular function: protein binding