TRNAU1AP

tRNA selenocysteine 1 associated protein 1, the group of RNA binding motif containing

Basic information

Region (hg38): 1:28553085-28578545

Previous symbols: [ "TRSPAP1" ]

Links

ENSG00000180098 ∙ NCBI:54952 ∙ OMIM:619597 ∙ HGNC:30813 ∙ Uniprot:Q9NX07 ∙ 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 TRNAU1AP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TRNAU1AP 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in TRNAU1AP

This is a list of pathogenic ClinVar variants found in the TRNAU1AP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-28553121-G-A		not specified	Uncertain significance (May 25, 2022)
1-28553734-C-A		not specified	Uncertain significance (May 18, 2023)
1-28560713-C-A		not specified	Uncertain significance (Jan 03, 2024)
1-28561368-A-T		not specified	Uncertain significance (Jul 14, 2021)
1-28564711-A-T		not specified	Uncertain significance (Apr 09, 2024)
1-28564785-C-G		not specified	Uncertain significance (Feb 13, 2024)
1-28567296-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-28567397-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-28571871-A-T		not specified	Uncertain significance (Oct 30, 2023)
1-28577526-G-A		not specified	Uncertain significance (Aug 21, 2023)
1-28577534-C-A		not specified	Uncertain significance (Mar 02, 2023)
1-28577536-A-G		not specified	Uncertain significance (Mar 20, 2024)
1-28577544-A-G		not specified	Uncertain significance (Apr 22, 2022)
1-28577545-T-C		not specified	Uncertain significance (May 28, 2024)
1-28577571-G-A		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TRNAU1AP	protein_coding	protein_coding	ENST00000373830	9	25455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000244	0.984	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	105	166	0.634	0.00000866	1889
Missense in Polyphen		22	39.775	0.55311		506
Synonymous	-0.555	67	61.5	1.09	0.00000337	509
Loss of Function	2.13	9	19.0	0.473	9.96e-7	216

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the early steps of selenocysteine biosynthesis and tRNA(Sec) charging to the later steps resulting in the cotranslational incorporation of selenocysteine into selenoproteins. Stabilizes the SECISBP2, EEFSEC and tRNA(Sec) complex. May be involved in the methylation of tRNA(Sec). Enhances efficiency of selenoproteins synthesis (By similarity). {ECO:0000250, ECO:0000269|PubMed:16508009}.
• Pathway: Selenium Metabolism and Selenoproteins (Consensus)

Recessive Scores

• pRec: 0.0824

Intolerance Scores

• loftool: 0.347
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.11

Haploinsufficiency Scores

• pHI: 0.0680
• hipred: Y
• hipred_score: 0.686
• ghis: 0.547

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.438

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trnau1ap
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); normal 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)

Gene ontology

• Biological process: selenocysteine incorporation
• Cellular component: nucleus;cytoplasm
• Molecular function: RNA binding