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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
USB1
U6 snRNA biogenesis phosphodiesterase 1
Chromosome 16 Β· 16q21
NCBI Gene: 79650Ensembl: ENSG00000103005.13HGNC: HGNC:25792UniProt: H3BN52
43PubMed Papers
21Diseases
0Drugs
28Pathogenic Variants
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
3'-5'-RNA exonuclease activitynucleusnucleoplasmprotein bindingpoikiloderma with neutropeniadyskeratosis congenitaparaneoplastic neurologic syndromegenetic disorder
✦AI Summary

USB1 (U6 snRNA biogenesis phosphodiesterase 1) is a 3'-5' RNA exonuclease that trims the 3' ends of pre-U6 small nuclear RNA (snRNA), generating a mature U6 snRNA molecule terminated with a 2',3'-cyclic phosphate 12. This processing is essential for preventing U6 snRNA degradation and enabling proper spliceosome assembly 1. Beyond U6 snRNA maturation, USB1 functions as a microRNA deadenylase that preferentially removes adenylated tails from miRNA 3' ends with 20-fold greater efficiency than uridine removal 23. This deadenylase activity protects non-coding RNAs from degradation 4. Loss-of-function USB1 mutations cause poikiloderma with neutropenia (PN), a rare autosomal recessive disorder characterized by skin abnormalities, chr16 neutropenia, and increased infection/malignancy risk 5. PN-associated mutations impair hematopoietic development through dysregulated miRNA levels during blood development 3, and can cause skin fragility through downregulation of basement membrane zone genes 6. The molecular pathogenesis involves aberrant adenylation of U6 snRNA and dysregulation of miRNA processing when USB1 function is compromised 23. Therapeutic approaches targeting USB1's interaction partner PAPD5/7 may rescue hematopoiesis in PN patients 3.

Sources cited
1
USB1 processes U6 RNA through cyclic phosphodiesterase activity and is essential for U6 snRNP assembly and spliceosome function
PMID: 28887445
2
USB1 removes 3' adenosines from U6 snRNA with 20-fold greater efficiency than uridines and generates 2',3'-cyclic phosphate terminals
PMID: 30215753
3
USB1 acts as a miRNA deadenylase and PN-associated mutations cause hematopoietic failure through dysregulated miRNA levels
PMID: 36862787
4
USB1 removes oligo(A) tails to protect non-coding RNAs from decay; loss-of-function mutations cause poikiloderma with neutropenia
PMID: 37544646
5
USB1 mutations cause skin fragility through downregulation of basement membrane zone genes and are associated with epidermolysis bullosa-like phenotypes
PMID: 34004352
6
Poikiloderma with neutropenia is caused by USB1 pathogenic variants and presents with skin abnormalities, chronic neutropenia, and endocrine involvement
PMID: 40289594
Disease Associationsβ“˜21
poikiloderma with neutropeniaOpen Targets
0.77Strong
dyskeratosis congenitaOpen Targets
0.47Moderate
paraneoplastic neurologic syndromeOpen Targets
0.37Weak
genetic disorderOpen Targets
0.19Weak
metabolic diseaseOpen Targets
0.07Suggestive
lymphatic malformation 11Open Targets
0.05Suggestive
hereditary angioedemaOpen Targets
0.04Suggestive
lymphatic malformation 8Open Targets
0.04Suggestive
chronic obstructive pulmonary diseaseOpen Targets
0.04Suggestive
hereditary angioedema with normal C1InhOpen Targets
0.04Suggestive
LipedemaOpen Targets
0.04Suggestive
lymphatic malformation 14Open Targets
0.03Suggestive
Milroy diseaseOpen Targets
0.03Suggestive
lymphatic malformation 7Open Targets
0.03Suggestive
neoplasmOpen Targets
0.02Suggestive
pulmonary arterial hypertensionOpen Targets
0.02Suggestive
SepsisOpen Targets
0.02Suggestive
neutropeniaOpen Targets
0.01Suggestive
cancerOpen Targets
0.01Suggestive
triple-negative breast cancerOpen Targets
0.01Suggestive
Poikiloderma with neutropeniaUniProt
Pathogenic Variants28
NM_024598.4(USB1):c.63del (p.Met22fs)Pathogenic
not provided|Poikiloderma with neutropenia|USB1-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 22
NM_024598.4(USB1):c.266-1G>APathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜…β˜†β˜†2024
NM_024598.4(USB1):c.623A>G (p.His208Arg)Likely pathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜…β˜†β˜†2023β†’ Residue 208
NM_024598.4(USB1):c.193del (p.Thr65fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2026β†’ Residue 65
NM_024598.4(USB1):c.673C>T (p.Gln225Ter)Pathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 225
NM_024598.4(USB1):c.499del (p.Thr167fs)Pathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 167
NM_024598.4(USB1):c.489_492del (p.Asn163fs)Pathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 163
NM_024598.4(USB1):c.693+1G>TPathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜†β˜†β˜†2024
NM_024598.4(USB1):c.418_449+5delLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_024598.4(USB1):c.503+1G>ALikely pathogenic
not provided
β˜…β˜†β˜†β˜†2024
NM_024598.4(USB1):c.415C>T (p.Gln139Ter)Pathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 139
NM_024598.4(USB1):c.99-2A>GLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2023
NM_024598.4(USB1):c.176_177del (p.Gly59fs)Pathogenic
Poikiloderma with neutropenia|not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 59
NM_024598.4(USB1):c.267T>G (p.Tyr89Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 89
NM_024598.4(USB1):c.430del (p.Arg144fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 144
NM_024598.4(USB1):c.87_98+13delLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2022
NM_024598.4(USB1):c.450-1G>CLikely pathogenic
not provided
β˜…β˜†β˜†β˜†2022
NM_024598.4(USB1):c.206del (p.Gly69fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2020β†’ Residue 69
NM_024598.4(USB1):c.481del (p.Tyr161fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2017β†’ Residue 161
NM_024598.4(USB1):c.345del (p.Arg115_Met116insTer)Likely pathogenic
Poikiloderma with neutropenia
β˜…β˜†β˜†β˜†2016β†’ Residue 115
View on ClinVar β†—
Related Genes
RECQL4Protein interaction91%SNW1Protein interaction88%PLRG1Protein interaction86%GPATCH1Protein interaction79%CDC5LProtein interaction79%PPIEProtein interaction79%
Tissue Expression6 tissues
Liver
100%
Lung
96%
Brain
72%
Heart
71%
Bone Marrow
68%
Ovary
46%
Gene Interaction Network
Click a node to explore
USB1RECQL4SNW1PLRG1GPATCH1CDC5LPPIE
PROTEIN STRUCTURE
Preparing viewer…
PDB4H7W Β· 1.10 Γ… Β· X-ray
View on RCSB β†—
Constraintβ“˜
LOEUFβ“˜
1.02LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.69 [0.48–1.02]
RankingsWhere USB1 stands among ~20K protein-coding genes
  • #9,817of 20,598
    Most Researched43
  • #1,877of 5,498
    Most Pathogenic Variants28
  • #9,937of 17,882
    Most Constrained (LOEUF)1.02
Genes detectedUSB1
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
The PARN, TOE1, and USB1 RNA deadenylases and their roles in non-coding RNA regulation.
PMID: 37544646
J Biol Chem Β· 2023
1.00
2
USB1 is a miRNA deadenylase that regulates hematopoietic development.
PMID: 36862787
Science Β· 2023
0.90
3
Kindler epidermolysis bullosa-like skin phenotype and downregulated basement membrane zone gene expression in poikiloderma with neutropenia and a homozygous USB1 mutation.
PMID: 34004352
Matrix Biol Β· 2021
0.80
4
Rothmund-Thomson Syndrome: novel pathogenic mutations and frequencies of variants in the RECQL4 and USB1 (C16orf57) gene.
PMID: 27247962
Mol Genet Genomic Med Β· 2016
0.70
5
Usb1 controls U6 snRNP assembly through evolutionarily divergent cyclic phosphodiesterase activities.
PMID: 28887445
Nat Commun Β· 2017
0.60