TXNDC16

thioredoxin domain containing 16, the group of Thioredoxin domain containing

Basic information

Region (hg38): 14:52430595-52552522

Previous symbols: [ "KIAA1344" ]

Links

ENSG00000087301 ∙ NCBI:57544 ∙ OMIM:616179 ∙ HGNC:19965 ∙ Uniprot:Q9P2K2 ∙ 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 TXNDC16 gene.

• Inborn genetic diseases (26 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC16 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				1		1
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	2	0

Variants in TXNDC16

This is a list of pathogenic ClinVar variants found in the TXNDC16 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-52432407-A-G		not specified	Uncertain significance (Jul 05, 2023)
14-52432428-G-A		not specified	Uncertain significance (Apr 22, 2022)
14-52432498-T-C		not specified	Uncertain significance (Apr 08, 2023)
14-52432515-G-A		not specified	Uncertain significance (Sep 25, 2023)
14-52432551-G-A		not specified	Uncertain significance (Mar 21, 2022)
14-52432583-A-C		not specified	Uncertain significance (Mar 13, 2023)
14-52439224-G-A		not specified	Uncertain significance (Sep 26, 2023)
14-52439273-G-T		not specified	Uncertain significance (Dec 19, 2022)
14-52439299-C-T		not specified	Uncertain significance (Feb 22, 2023)
14-52439324-C-T		not specified	Uncertain significance (Aug 16, 2022)
14-52455376-G-A		not specified	Uncertain significance (Dec 14, 2023)
14-52455433-G-A		not specified	Uncertain significance (Nov 01, 2022)
14-52455445-G-A		not specified	Likely benign (Jun 06, 2022)
14-52457135-C-T		not specified	Uncertain significance (Nov 08, 2022)
14-52457148-T-G		not specified	Uncertain significance (Dec 01, 2022)
14-52470087-A-G		not specified	Likely benign (Oct 20, 2023)
14-52470130-C-T		not specified	Uncertain significance (Jul 20, 2022)
14-52470567-G-C		not specified	Uncertain significance (Mar 20, 2023)
14-52470627-A-C		not specified	Uncertain significance (Nov 27, 2023)
14-52470669-T-C		not specified	Uncertain significance (Oct 03, 2022)
14-52470671-G-A		not specified	Uncertain significance (May 24, 2023)
14-52482262-T-C		not specified	Uncertain significance (Jul 21, 2021)
14-52482847-G-C		not specified	Uncertain significance (Feb 26, 2024)
14-52482863-G-A		not specified	Uncertain significance (Jul 21, 2022)
14-52482894-C-G		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC16	protein_coding	protein_coding	ENST00000281741	19	121933

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000995	1.00	125687	0	54	125741	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.243	416	402	1.03	0.0000185	5391
Missense in Polyphen		87	81.357	1.0694		1091
Synonymous	-1.10	161	144	1.12	0.00000692	1540
Loss of Function	3.34	15	36.9	0.407	0.00000156	534

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000396	0.000392
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000278	0.000272
South Asian	0.000473	0.000457
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0903

Intolerance Scores

• loftool: 0.835
• rvis_EVS: 0.83
• rvis_percentile_EVS: 88.11

Haploinsufficiency Scores

• pHI: 0.124
• hipred: N
• hipred_score: 0.172
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc16

Gene ontology

• Biological process: biological_process;cell redox homeostasis
• Cellular component: endoplasmic reticulum lumen;extracellular exosome
• Molecular function: protein binding