TSR2

TSR2 ribosome maturation factor, the group of Ribosomal biogenesis factors

Basic information

Region (hg38): X:54440404-54448032

Links

ENSG00000158526NCBI:90121OMIM:300945HGNC:25455Uniprot:Q969E8AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Diamond-Blackfan anemia (Supportive), mode of inheritance: AD
  • Diamond-Blackfan anemia 14 with mandibulofacial dysostosis (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Diamond-Blackfan anemia 14 with mandibulofacial dysostosisXLAudiologic/Otolaryngologic; Hematologic; OncologicEarly recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Specific treatment of anemia (eg, steroids, regular transfusions) can be effective; surveillance for and early treatment of malignancy may be beneficial; Individuals with DBA may manifest a variety of congenital malformations, and awareness may allow prompt detection and managementAudiologic/Otolaryngologic; Craniofacial; Genitourinary; Hematologic; Musculoskeletal; Oncologic11424144; 24942156

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TSR2 gene.

  • Diamond-Blackfan anemia 15 with mandibulofacial dysostosis (1 variants)
  • not provided (1 variants)
  • Diamond-Blackfan anemia 14 with mandibulofacial dysostosis (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TSR2 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
6
clinvar
4
clinvar
1
clinvar
11
missense
1
clinvar
20
clinvar
1
clinvar
22
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
3
3
non coding
1
clinvar
6
clinvar
32
clinvar
27
clinvar
6
clinvar
72
Total 2 6 58 31 8

Variants in TSR2

This is a list of pathogenic ClinVar variants found in the TSR2 region.

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

Position Type Phenotype Significance ClinVar
X-54440428-G-A Uncertain significance (Aug 24, 2022)2414349
X-54440433-T-C TSR2-related disorder Likely benign (Jan 23, 2025)2076580
X-54440435-C-T not specified Uncertain significance (Jul 19, 2022)2302057
X-54440438-A-G TSR2-related disorder Uncertain significance (Oct 05, 2022)2635895
X-54440443-G-C not specified Uncertain significance (Nov 10, 2024)2262503
X-54440446-C-A Uncertain significance (Jun 26, 2023)2867263
X-54440466-G-T Uncertain significance (Oct 24, 2022)2059210
X-54440482-G-C not specified Uncertain significance (Aug 22, 2023)2621096
X-54440509-G-GGGGCCA Likely benign (May 28, 2024)3716930
X-54440522-G-A Likely benign (Jul 01, 2024)3698163
X-54440632-C-T Benign (May 22, 2021)1269390
X-54440690-A-G Uncertain significance (Nov 07, 2023)2798751
X-54440712-G-C Uncertain significance (Jan 22, 2025)1695305
X-54440746-G-C Uncertain significance (Aug 04, 2023)2191008
X-54440751-G-A Benign (Oct 06, 2023)2150704
X-54440774-C-A Uncertain significance (Oct 01, 2023)2660661
X-54440774-C-T not specified Uncertain significance (Oct 30, 2024)3251902
X-54440775-G-T Uncertain significance (Oct 22, 2024)2775965
X-54440776-C-G Uncertain significance (Sep 19, 2023)2822709
X-54440783-G-A Uncertain significance (Nov 14, 2024)3725274
X-54440800-C-A Likely benign (Jun 22, 2024)1974498
X-54443382-C-G Likely benign (Nov 02, 2024)3680570
X-54443394-A-G Likely benign (Dec 02, 2024)2179140
X-54443414-G-C Uncertain significance (May 21, 2023)2787332
X-54443418-A-G Diamond-Blackfan anemia 14 with mandibulofacial dysostosis • Diamond-Blackfan anemia 15 with mandibulofacial dysostosis Pathogenic (May 19, 2015)187847

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
TSR2protein_codingprotein_codingENST00000375151 55087
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.8010.19400000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9894466.70.6590.000004651259
Missense in Polyphen514.730.33943284
Synonymous-0.6353025.91.160.00000197362
Loss of Function2.1405.340.003.37e-799

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in 20S pre-rRNA processing. {ECO:0000305}.;
Disease
DISEASE: Diamond-Blackfan anemia 14, with mandibulofacial dysostosis (DBA14) [MIM:300946]: A form of Diamond-Blackfan anemia, a congenital non-regenerative hypoplastic anemia that usually presents early in infancy. Diamond-Blackfan anemia is characterized by a moderate to severe macrocytic anemia, erythroblastopenia, and an increased risk of malignancy. 30 to 40% of Diamond-Blackfan anemia patients present with short stature and congenital anomalies, the most frequent being craniofacial (Pierre-Robin syndrome and cleft palate), thumb and urogenital anomalies. {ECO:0000269|PubMed:24942156}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.109

Intolerance Scores

loftool
rvis_EVS
0.01
rvis_percentile_EVS
54.63

Haploinsufficiency Scores

pHI
0.115
hipred
N
hipred_score
0.335
ghis
0.605

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.731

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Tsr2
Phenotype

Zebrafish Information Network

Gene name
tsr2
Affected structure
ceratohyal cartilage
Phenotype tag
abnormal
Phenotype quality
bent

Gene ontology

Biological process
maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
Cellular component
Molecular function
protein binding