CLP1

Chr 11q12.1

cleavage factor polyribonucleotide kinase subunit 1

Aliases:: HEAB, hClp1
MANE:: ENST00000533682.2

OMIM: 608757 ↗NCBI: 10978 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

CLP1 · Q92989

v62025-08-01

Predicted Aligned Error matrix for CLP1 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

93.8/ 100

Very high

425 residues

Confidence breakdown

Very high(≥ 90)89%
Confident(70–90)7%
Low(50–70)2%
Very low(< 50)2%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Ataxia and cerebellar anomalies - narrow panel
BIALLELIC, autosomal or pseudoautosomal
Cerebellar hypoplasia
BIALLELIC, autosomal or pseudoautosomal
DDG2P
BIALLELIC, autosomal or pseudoautosomal
Fetal anomalies
BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia
BIALLELIC, autosomal or pseudoautosomal
Hereditary neuropathy or pain disorder
BIALLELIC, autosomal or pseudoautosomal
Intellectual disability
BIALLELIC, autosomal or pseudoautosomal
Hereditary ataxia with onset in adulthood
BIALLELIC, autosomal or pseudoautosomal

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Disease associations (Open Targets)

pontocerebellar hypoplasia type 10
0.80
pontocerebellar hypoplasia
0.46
dengue disease
0.37
Non-syndromic pontocerebellar hypoplasia
0.35
hereditary disease
0.19
urinary bladder carcinoma
0.19
bladder transitional cell carcinoma
0.19
head and neck squamous cell carcinoma
0.19
breast carcinoma
0.19
small cell lung carcinoma
0.18

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Polyribonucleotide 5'-hydroxyl-kinase Clp1

Polynucleotide kinase that can phosphorylate the 5'-hydroxyl groups of double-stranded RNA (dsRNA), single-stranded RNA (ssRNA), double-stranded DNA (dsDNA) and double-stranded DNA:RNA hybrids. dsRNA is phosphorylated more efficiently than dsDNA, and the RNA component of a DNA:RNA hybrid is phosphorylated more efficiently than the DNA component. Plays a key role in both tRNA splicing and mRNA 3'-end formation. Component of the tRNA splicing endonuclease complex: phosphorylates the 5'-terminus of the tRNA 3'-exon during tRNA splicing; this phosphorylation event is a prerequisite for the subsequent ligation of the two exon halves and the production of a mature tRNA (PubMed:24766809, PubMed:24766810). Its role in tRNA splicing and maturation is required for cerebellar development (PubMed:24766809, PubMed:24766810). Component of the pre-mRNA cleavage complex II (CF-II), which seems to be required for mRNA 3'-end formation. Also phosphorylates the 5'-terminus of exogenously introduced short interfering RNAs (siRNAs), which is a necessary prerequisite for their incorporation into the RNA-induced silencing complex (RISC). However, endogenous siRNAs and microRNAs (miRNAs) that are produced by the cleavage of dsRNA precursors by DICER1 already contain a 5'-phosphate group, so this protein may be dispensible for normal RNA-mediated gene silencing