TTC23

tetratricopeptide repeat domain 23, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 15:99136322-99251223

Links

ENSG00000103852 ∙ NCBI:64927 ∙ ∙ HGNC:25730 ∙ Uniprot:Q5W5X9 ∙ 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 TTC23 gene.

• Orofaciodigital syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC23 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in TTC23

This is a list of pathogenic ClinVar variants found in the TTC23 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-99218714-C-A		Orofaciodigital syndrome	Benign (Jun 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC23	protein_coding	protein_coding	ENST00000394132	10	114901

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.38e-24	0.0000310	125566	2	180	125748	0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0600	239	242	0.989	0.0000126	2902
Missense in Polyphen		52	56.101	0.92691		715
Synonymous	-0.565	102	95.0	1.07	0.00000537	866
Loss of Function	-1.42	31	23.6	1.31	0.00000116	287

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00155	0.00155
Ashkenazi Jewish	0.000398	0.000397
East Asian	0.000598	0.000598
Finnish	0.000326	0.000323
European (Non-Finnish)	0.000698	0.000695
Middle Eastern	0.000598	0.000598
South Asian	0.00128	0.00124
Other	0.000820	0.000815

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.988
• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.0976
• hipred: N
• hipred_score: 0.123
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc23

Gene ontology

• Molecular function: protein binding