TXNDC15

thioredoxin domain containing 15, the group of Thioredoxin domain containing

Basic information

Region (hg38): 5:134874371-134901635

Previous symbols: [ "C5orf14" ]

Links

ENSG00000113621 ∙ NCBI:79770 ∙ OMIM:617778 ∙ HGNC:20652 ∙ Uniprot:Q96J42 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Meckel syndrome (Supportive), mode of inheritance: AR
• Meckel syndrome (Moderate), mode of inheritance: AR
• meckel syndrome 14 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Meckel syndrome 14	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular; Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal	27894351; 30851085; 31411728

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TXNDC15 gene.

• Meckel syndrome 14 (2 variants)
• Meckel-Gruber syndrome (2 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TXNDC15 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				6	2	8
missense			19	2	1	22
nonsense	2					2
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1					1
splice region				1		1
non coding					3	3
Total	3	0	20	8	6

Highest pathogenic variant AF is 0.0000394

Variants in TXNDC15

This is a list of pathogenic ClinVar variants found in the TXNDC15 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-134874433-C-T			Likely benign (Feb 04, 2022)
5-134874454-G-T		TXNDC15-related disorder	Likely benign (Feb 18, 2019)
5-134874469-G-A			Likely benign (Apr 03, 2023)
5-134874512-C-G		TXNDC15-related disorder	Likely benign (Feb 02, 2021)
5-134874531-G-A		Meckel-Gruber syndrome • Meckel syndrome 14	Pathogenic (Mar 14, 2024)
5-134875365-GA-G			Benign (Jan 01, 2023)
5-134875367-G-T			Benign (Jan 01, 2023)
5-134887684-GC-G			Benign (Nov 27, 2023)
5-134887695-T-C		Inborn genetic diseases	Uncertain significance (Jul 26, 2022)
5-134887788-A-G		Inborn genetic diseases	Uncertain significance (May 20, 2024)
5-134887794-C-T		Inborn genetic diseases	Uncertain significance (Feb 16, 2023)
5-134887800-G-GC		Meckel syndrome 14	Pathogenic (May 13, 2022)
5-134887831-G-A			Benign (Aug 17, 2023)
5-134887855-C-T			Likely benign (Oct 13, 2022)
5-134887895-G-C		Meckel-Gruber syndrome	Uncertain significance (May 25, 2020)
5-134887903-A-G			Benign (Jan 29, 2024)
5-134887908-G-C		Inborn genetic diseases	Uncertain significance (Jan 23, 2024)
5-134887922-G-A		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
5-134887925-G-A		Inborn genetic diseases	Uncertain significance (Jun 21, 2023)
5-134887947-C-T		Inborn genetic diseases	Uncertain significance (Nov 17, 2023)
5-134887967-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 06, 2022)
5-134887970-C-T			Pathogenic (Jul 01, 2020)
5-134887974-A-G		Inborn genetic diseases	Conflicting classifications of pathogenicity (May 20, 2024)
5-134887996-C-T			Likely benign (Nov 10, 2023)
5-134888015-G-T		Inborn genetic diseases	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TXNDC15	protein_coding	protein_coding	ENST00000358387	5	27723

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00965	0.981	125700	0	48	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.563	185	208	0.890	0.0000111	2340
Missense in Polyphen		44	55.278	0.79598		690
Synonymous	0.615	77	84.2	0.915	0.00000497	735
Loss of Function	2.26	6	15.7	0.383	8.94e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000214
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000308	0.000308
Middle Eastern	0.000163	0.000163
South Asian	0.0000664	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• loftool: 0.492
• rvis_EVS: -0.27
• rvis_percentile_EVS: 34.32

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.465
• ghis: 0.586

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.263

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Txndc15

Gene ontology

• Biological process: cell redox homeostasis
• Cellular component: cell;integral component of membrane