TTC31

tetratricopeptide repeat domain 31, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 2:74483072-74494559

Links

ENSG00000115282 ∙ NCBI:64427 ∙ ∙ HGNC:25759 ∙ Uniprot:Q49AM3 ∙ 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 TTC31 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TTC31 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			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	0

Variants in TTC31

This is a list of pathogenic ClinVar variants found in the TTC31 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74483114-A-G		not specified	Likely benign (Dec 13, 2023)
2-74483378-A-G		not specified	Uncertain significance (Dec 15, 2021)
2-74483408-G-A		not specified	Uncertain significance (Jan 06, 2023)
2-74490035-A-C		not specified	Uncertain significance (Aug 03, 2022)
2-74490040-C-T		not specified	Uncertain significance (Oct 04, 2022)
2-74490044-G-A		not specified	Uncertain significance (Oct 13, 2023)
2-74490046-C-G		not specified	Uncertain significance (Apr 24, 2024)
2-74490080-G-A		not specified	Uncertain significance (Apr 04, 2024)
2-74490103-G-A		not specified	Uncertain significance (Apr 18, 2024)
2-74490124-C-A		not specified	Uncertain significance (Mar 31, 2023)
2-74490270-G-C		not specified	Uncertain significance (Dec 14, 2023)
2-74490330-T-C		not specified	Uncertain significance (Apr 07, 2023)
2-74490339-C-T		not specified	Uncertain significance (Dec 13, 2023)
2-74490415-G-A		not specified	Uncertain significance (May 13, 2024)
2-74490417-G-A		not specified	Uncertain significance (Feb 02, 2023)
2-74490427-G-T		not specified	Uncertain significance (Mar 29, 2023)
2-74490665-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-74490698-C-T		not specified	Uncertain significance (Aug 14, 2023)
2-74490726-G-A		not specified	Uncertain significance (Dec 14, 2022)
2-74491155-C-T		not specified	Uncertain significance (Jun 10, 2024)
2-74491180-C-T		not specified	Uncertain significance (Jan 16, 2024)
2-74491317-A-T		not specified	Uncertain significance (Sep 22, 2022)
2-74491509-T-C		not specified	Uncertain significance (Jan 03, 2024)
2-74491541-C-A		not specified	Uncertain significance (Sep 16, 2021)
2-74491541-C-T		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TTC31	protein_coding	protein_coding	ENST00000233623	13	11814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.29e-16	0.0157	124730	0	68	124798	0.000272

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.354	314	297	1.06	0.0000168	3294
Missense in Polyphen		77	66.563	1.1568		784
Synonymous	1.49	92	112	0.821	0.00000538	1088
Loss of Function	0.289	25	26.6	0.940	0.00000137	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00159	0.00156
Ashkenazi Jewish	0.00	0.00
East Asian	0.000292	0.000278
Finnish	0.000232	0.000232
European (Non-Finnish)	0.000207	0.000203
Middle Eastern	0.000292	0.000278
South Asian	0.000197	0.000196
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.860
• rvis_EVS: 1.27
• rvis_percentile_EVS: 93.6

Haploinsufficiency Scores

• pHI: 0.0805
• hipred: N
• hipred_score: 0.112
• ghis: 0.460

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.720

Gene Damage Prediction

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