TSR3

TSR3 ribosome maturation factor, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): 16:1349240-1351878

Previous symbols: [ "C16orf42" ]

Links

ENSG00000007520 ∙ NCBI:115939 ∙ OMIM:617058 ∙ HGNC:14175 ∙ Uniprot:Q9UJK0 ∙ 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 TSR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSR3 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	2		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	25	3	1

Variants in TSR3

This is a list of pathogenic ClinVar variants found in the TSR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1349451-G-A		not specified	Uncertain significance (Jul 19, 2022)
16-1349453-T-G		not specified	Uncertain significance (Mar 24, 2023)
16-1349473-C-G		not specified	Uncertain significance (Oct 03, 2022)
16-1349479-C-T			Likely benign (Jun 01, 2022)
16-1349501-C-G		not specified	Uncertain significance (Jun 28, 2022)
16-1349501-C-T		not specified	Likely benign (Aug 10, 2023)
16-1349543-C-T		not specified	Uncertain significance (Sep 14, 2023)
16-1349549-C-T		not specified	Likely benign (Dec 17, 2021)
16-1349579-G-A		not specified	Uncertain significance (Apr 25, 2023)
16-1349941-C-G		not specified	Uncertain significance (Nov 21, 2023)
16-1350077-G-T		not specified	Uncertain significance (Jan 09, 2024)
16-1350135-C-T		not specified	Uncertain significance (Jan 06, 2023)
16-1350144-G-A		not specified	Uncertain significance (Feb 28, 2023)
16-1350145-C-G		not specified	Uncertain significance (Oct 05, 2023)
16-1350166-G-A		not specified	Uncertain significance (May 30, 2024)
16-1350205-G-A		not specified	Uncertain significance (Dec 27, 2023)
16-1350855-A-C		not specified	Uncertain significance (Nov 07, 2022)
16-1350858-G-A		not specified	Uncertain significance (Feb 26, 2024)
16-1350861-G-A		not specified	Uncertain significance (Oct 12, 2021)
16-1350867-A-G		not specified	Uncertain significance (Aug 29, 2022)
16-1350910-G-C		not specified	Uncertain significance (Apr 06, 2024)
16-1350932-A-G		not specified	Uncertain significance (Feb 28, 2023)
16-1350943-G-C		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
16-1350986-T-G		not specified	Uncertain significance (Mar 08, 2024)
16-1350998-T-G		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TSR3	protein_coding	protein_coding	ENST00000007390	6	2672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00114	0.850	125510	0	22	125532	0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.502	189	171	1.11	0.0000108	1958
Missense in Polyphen		46	49.764	0.92435		527
Synonymous	0.389	75	79.4	0.944	0.00000555	659
Loss of Function	1.25	6	10.3	0.581	5.25e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000182
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000990	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable pre-rRNA processing protein involved in ribosome biogenesis. {ECO:0000255|HAMAP-Rule:MF_03146}.
• Pathway: rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.92

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.197
• ghis: 0.560

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tsr3

Gene ontology

• Biological process: rRNA modification;maturation of SSU-rRNA
• Cellular component: cytosol
• Molecular function: transferase activity