TSR3

protein-coding

TSR3 ribosome maturation factor, the group of Ribosomal biogenesis factors

Gene summary

Enables rRNA small subunit aminocarboxypropyltransferase activity. Involved in enzyme-directed rRNA pseudouridine synthesis. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C16orf42

MANE transcript

NM_001001410.3

Inheritance

—

ClinVar variants

U:70B:4

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 0.58

Max pathogenic AF

—

Genomic locus

chr16:1,349,240-1,351,878

External References & Databases

Ensembl (ENSG00000007520)

Transcript & Mutation Effects

hg38 • Region Span ~2.6 kb

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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 TSR3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 65

not providedTotal: 1

Inborn genetic diseasesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001410.3. 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 clinvar		2
missense			66 clinvar	3 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	70	4	0	74

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001410.3	RefSeq	NP_001001410.1	6	MANE Select
ENST00000007390.3	Ensembl	ENSP00000007390.2	6	MANE Select
ENST00000566296.1	Ensembl	ENSP00000455722.1	3	Standard
ENST00000858635.1	Ensembl	ENSP00000528694.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

rRNA processing
Metabolism of RNA
rRNA modification in the nucleus and cytosol
rRNA processing in the nucleus and cytosol

Biological Process

rRNA modification
maturation of SSU-rRNA

Molecular Function

transferase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000007390
Coding exons: 6
Length: 2672
Individuals with no LoFs: 125510
Homozygous LoFs: 0
Heterozygous LoFs: 22
Defined: 125532
p: 0.0000876

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.502	189	171	1.11	0.0000108	1958
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.000099	0.000098	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable pre-rRNA processing protein involved in ribosome biogenesis. {ECO:0000255|HAMAP-Rule:MF_03146}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

RVIS EVS: -0.03
RVIS percentile EVS: 51.92

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N

Gene Damage Prediction

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