THADA

THADA armadillo repeat containing, the group of Armadillo repeat containing

Basic information

Region (hg38): 2:43230851-43596038

Links

ENSG00000115970 ∙ NCBI:63892 ∙ OMIM:611800 ∙ HGNC:19217 ∙ Uniprot:Q6YHU6 ∙ 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 THADA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the THADA 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				17	4	21
missense			131	19	12	162
nonsense						0
start loss						0
frameshift						0
inframe indel				1	2	3
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding					1	1
Total	0	0	131	37	19

Variants in THADA

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

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

Position	Type	Phenotype	Significance	ClinVar
2-43230958-G-A		not specified	Uncertain significance (Dec 28, 2022)
2-43230958-G-C		THADA-related disorder	Likely benign (Jun 10, 2019)
2-43230964-G-C		not specified	Uncertain significance (Nov 29, 2021)
2-43230994-G-A		not specified	Uncertain significance (Nov 17, 2022)
2-43230999-A-G		THADA-related disorder	Likely benign (Aug 15, 2019)
2-43231001-A-C		not specified	Uncertain significance (Oct 20, 2024)
2-43231029-T-A		not specified	Uncertain significance (Nov 14, 2023)
2-43231099-A-G		not specified	Uncertain significance (Mar 24, 2023)
2-43231126-A-C		not specified	Uncertain significance (Oct 03, 2022)
2-43231142-G-A		not specified	Uncertain significance (Nov 17, 2023)
2-43231151-TGAA-T		THADA-related disorder	Likely benign (Feb 01, 2023)
2-43231162-G-C		not specified	Uncertain significance (Dec 06, 2022)
2-43231235-C-T		not specified	Likely benign (Jul 16, 2024)
2-43231255-A-G		not specified	Uncertain significance (May 08, 2023)
2-43231262-G-A		not specified	Uncertain significance (Oct 30, 2023)
2-43231264-T-C		not specified	Uncertain significance (Mar 21, 2024)
2-43231280-C-T			Uncertain significance (Feb 05, 2021)
2-43231306-T-C		not specified	Uncertain significance (Dec 14, 2021)
2-43231327-A-G		not specified	Uncertain significance (Dec 14, 2023)
2-43231328-G-A		THADA-related disorder	Likely benign (Jul 01, 2019)
2-43231335-T-G		THADA-related disorder	Benign (Sep 24, 2019)
2-43232739-C-T		not specified	Uncertain significance (Oct 03, 2023)
2-43232751-T-A		not specified	Uncertain significance (Jun 22, 2023)
2-43232781-G-C		not specified	Uncertain significance (Jul 14, 2022)
2-43232789-G-A		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
THADA	protein_coding	protein_coding	ENST00000405006	37	429386

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.62e-41	0.00206	124373	1	269	124643	0.00108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.96	1225	966	1.27	0.0000491	12704
Missense in Polyphen		278	228.47	1.2168		3106
Synonymous	-3.71	450	360	1.25	0.0000190	3683
Loss of Function	1.80	73	91.6	0.797	0.00000437	1213

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00211	0.00209
Ashkenazi Jewish	0.00	0.00
East Asian	0.00303	0.00301
Finnish	0.000279	0.000278
European (Non-Finnish)	0.00106	0.00102
Middle Eastern	0.00303	0.00301
South Asian	0.00130	0.00128
Other	0.00151	0.00132

dbNSFP

Source: dbNSFP

• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.0982

Intolerance Scores

• loftool: 1.00
• rvis_EVS: 0.45
• rvis_percentile_EVS: 77.98

Haploinsufficiency Scores

• pHI: 0.0992
• hipred: N
• hipred_score: 0.251
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.461

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Thada

Zebrafish Information Network

• Gene name: thada
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: tRNA methylation;negative regulation of endoplasmic reticulum calcium ion concentration;lipid homeostasis;negative regulation of calcium-transporting ATPase activity;adaptive thermogenesis
• Cellular component: cytosol;cytoplasmic side of endoplasmic reticulum membrane
• Molecular function: protein binding