TNPO3

transportin 3, the group of Armadillo like helical domain containing|Importins

Basic information

Region (hg38): 7:128954180-129055173

Previous symbols: [ "LGMD1F" ]

Links

ENSG00000064419

∙ NCBI:23534 ∙ OMIM:610032 ∙ HGNC:17103 ∙ Uniprot:Q9Y5L0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

autosomal dominant limb-girdle muscular dystrophy type 1F (Strong), mode of inheritance: AD
autosomal dominant limb-girdle muscular dystrophy type 1F (Supportive), mode of inheritance: AD
autosomal dominant limb-girdle muscular dystrophy type 1F (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Muscular dystrophy, limb-girdle, autosomal dominant 2	AD	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	Musculoskeletal	11222786; 23543484; 23667635

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TNPO3 gene.

Autosomal_dominant_limb-girdle_muscular_dystrophy_type_1F (572 variants)
not_provided (165 variants)
Inborn_genetic_diseases (60 variants)
not_specified (33 variants)
TNPO3-related_disorder (12 variants)
Scapular_winging (1 variants)
Muscular_dystrophy,_limb-girdle,_autosomal_dominant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNPO3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012470.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			7 clinvar	156 clinvar	3 clinvar	166
missense	1 clinvar	2 clinvar	301 clinvar	15 clinvar		319
nonsense	1 clinvar		11 clinvar			12
start loss			1			1
frameshift	1 clinvar	4 clinvar	15 clinvar			20
splice donor/acceptor (+/-2bp)		2 clinvar	9 clinvar			11
Total	3	8	344	171	3

Highest pathogenic variant AF is 0.0000105326

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNPO3	protein_coding	protein_coding	ENST00000265388	22	100251

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000175	1.00	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.44	300	521	0.576	0.0000286	6015
Missense in Polyphen		58	131.76	0.44021		1481
Synonymous	0.983	173	190	0.909	0.00000979	1826
Loss of Function	4.56	21	58.7	0.358	0.00000355	610

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000218	0.000217
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000187	0.000185
Middle Eastern	0.000218	0.000217
South Asian	0.000197	0.000196
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: Seems to function in nuclear protein import as nuclear transport receptor. In vitro, mediates the nuclear import of splicing factor SR proteins RBM4, SFRS1 and SFRS2, by recognizing phosphorylated RS domains. {ECO:0000269|PubMed:10366588, ECO:0000269|PubMed:10713112, ECO:0000269|PubMed:11517331, ECO:0000269|PubMed:12628928}.;

Recessive Scores

pRec: 0.114

Intolerance Scores

loftool: 0.301
rvis_EVS: -1.18
rvis_percentile_EVS: 5.94

Haploinsufficiency Scores

pHI: 0.608
hipred: Y
hipred_score: 0.526
ghis: 0.664

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Tnpo3
Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name: tnpo3
Affected structure: thymus
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: protein import into nucleus
Cellular component: nucleus;cytoplasm;intracellular membrane-bounded organelle
Molecular function: protein binding;protein transporter activity;signaling receptor activity;identical protein binding