TXNDC9

protein-coding

thioredoxin domain containing 9, the group of Thioredoxin domain containing

Gene summary

The protein encoded by this gene is a member of the thioredoxin family. The exact function of this protein is not known but it is associated with cell differentiation. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005783.4

Inheritance

—

ClinVar variants

U:22B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr2:99,318,982-99,340,702

External References & Databases

Ensembl (ENSG00000115514)

Transcript & Mutation Effects

hg38 • Region Span ~21.7 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TXNDC9 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005783.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			21 clinvar	1 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	22	1	0	23

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 29 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005783.4	RefSeq	NP_005774.2	4	MANE Select
ENST00000264255.8	Ensembl	ENSP00000264255.3	4	MANE Select
ENST00000409434.5	Ensembl	ENSP00000387275.1	3	Standard
ENST00000409434.6	Ensembl	ENSP00000387275.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
cell redox homeostasis

Molecular Function

protein binding
cadherin binding

Cellular Component

cellular_component
nucleus
centrosome
cytosol
midbody

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000264255
Coding exons: 4
Length: 21721
Individuals with no LoFs: 125738
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 125744
p: 0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.872	85	111	0.767	0.00000507	1504
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000031	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000098	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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