TXNDC9

thioredoxin domain containing 9, the group of Thioredoxin domain containing

Basic information

Region (hg38): 2:99318982-99340702

Links

ENSG00000115514 ∙ NCBI:10190 ∙ OMIM:612564 ∙ HGNC:24110 ∙ Uniprot:O14530 ∙ 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 TXNDC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC9 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in TXNDC9

This is a list of pathogenic ClinVar variants found in the TXNDC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-99319726-T-G		not specified	Uncertain significance (Oct 26, 2022)
2-99321973-G-A		not specified	Uncertain significance (Dec 20, 2023)
2-99322028-G-C		not specified	Uncertain significance (Mar 29, 2022)
2-99322130-T-C		not specified	Uncertain significance (Dec 07, 2021)
2-99322164-G-T		not specified	Uncertain significance (May 17, 2023)
2-99327537-G-C		not specified	Uncertain significance (Nov 22, 2023)
2-99333044-C-T		not specified	Likely benign (Apr 10, 2023)
2-99333074-C-T		not specified	Uncertain significance (May 11, 2022)
2-99333075-G-A		not specified	Uncertain significance (Nov 04, 2023)
2-99337578-G-C		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC9	protein_coding	protein_coding	ENST00000264255	4	21721

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.377	0.613	125738	0	6	125744	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.872	85	111	0.767	0.00000507	1504
Missense in Polyphen		18	23.736	0.75834		337
Synonymous	0.904	34	41.4	0.821	0.00000191	409
Loss of Function	2.17	2	9.07	0.221	3.79e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000310	0.0000310
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Significantly diminishes the chaperonin TCP1 complex ATPase activity, thus negatively impacts protein folding, including that of actin or tubulin. {ECO:0000269|PubMed:16415341}.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.471
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.81

Haploinsufficiency Scores

• pHI: 0.493
• hipred: N
• hipred_score: 0.267
• ghis: 0.418

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc9

Gene ontology

• Biological process: biological_process;cell redox homeostasis
• Cellular component: cellular_component;nucleus;centrosome;cytosol;midbody
• Molecular function: protein binding;cadherin binding