TTC38

tetratricopeptide repeat domain 38, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 22:46267961-46294008

Links

ENSG00000075234 ∙ NCBI:55020 ∙ ∙ HGNC:26082 ∙ Uniprot:Q5R3I4 ∙ 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 TTC38 gene.

• not_specified (75 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC38 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017931.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			72	5		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	72	5	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC38	protein_coding	protein_coding	ENST00000381031	14	26048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.26e-13	0.270	123881	18	991	124890	0.00405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.406	275	295	0.933	0.0000183	3058
Missense in Polyphen		71	78.665	0.90256		728
Synonymous	0.657	116	125	0.925	0.00000880	914
Loss of Function	1.12	23	29.6	0.777	0.00000160	301

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00149	0.00148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0122	0.0121
Finnish	0.000510	0.000510
European (Non-Finnish)	0.000444	0.000441
Middle Eastern	0.0122	0.0121
South Asian	0.0226	0.0223
Other	0.00281	0.00264

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0980

Intolerance Scores

• rvis_EVS: 0.91
• rvis_percentile_EVS: 89.54

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.216
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0245

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ttc38

Gene ontology

• Cellular component: extracellular exosome