TTC23

protein-coding

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

Gene summary

Predicted to be involved in positive regulation of smoothened signaling pathway. Predicted to be located in cilium. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001288615.3

Inheritance

—

ClinVar variants

U:8B:1

Top phenotype

Orofaciodigital syndrome

gnomAD constraint

pLI —, LoF o/e 1.31

Max pathogenic AF

—

Genomic locus

chr15:99,136,323-99,251,223

External References & Databases

Ensembl (ENSG00000103852)

Transcript & Mutation Effects

hg38 • Region Span ~114.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TTC23 variants in ClinVar

1 Conditions Cataloged

Orofaciodigital syndromeTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001288615.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			3 clinvar			3
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar		1 clinvar	5
Total	0	0	8	0	1	9

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 90 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001288615.3	RefSeq	NP_001275544.1	10	MANE Select
ENST00000394132.7	Ensembl	ENSP00000377690.2	10	MANE Select
NM_001288616.3	RefSeq	NP_001275545.1	10	Standard
NM_001353869.2	RefSeq	NP_001340798.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000394132
Coding exons: 10
Length: 114901
Individuals with no LoFs: 125566
Homozygous LoFs: 2
Heterozygous LoFs: 180
Defined: 125748
p: 0.000724

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0600	239	242	0.989	0.0000126	2902
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.00075	0.00072	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00060	0.00060	rare
Finnish	0.00033	0.00032	rare
European (Non-Finnish)	0.00070	0.00069	rare
South Asian	0.0013	0.0012	notable
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.988
RVIS EVS: -0.22
RVIS percentile EVS: 37.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.134

Gene Damage Prediction

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