Incidental Mutation 'R9351:Clp1'
ID 708051
Institutional Source Beutler Lab
Gene Symbol Clp1
Ensembl Gene ENSMUSG00000027079
Gene Name CLP1, cleavage and polyadenylation factor I subunit
Synonyms
MMRRC Submission
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9351 (G1)
Quality Score 225.009
Status Validated
Chromosome 2
Chromosomal Location 84553466-84557631 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 84554195 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Glutamic Acid at position 325 (K325E)
Ref Sequence ENSEMBL: ENSMUSP00000028475 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028475] [ENSMUST00000165219]
AlphaFold Q99LI9
Predicted Effect probably benign
Transcript: ENSMUST00000028475
AA Change: K325E

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000028475
Gene: ENSMUSG00000027079
AA Change: K325E

DomainStartEndE-ValueType
Pfam:CLP1_N 15 107 1.7e-36 PFAM
Pfam:CLP1_P 121 307 2e-79 PFAM
Pfam:Clp1 312 423 1.3e-34 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000165219
AA Change: K325E

PolyPhen 2 Score 0.015 (Sensitivity: 0.96; Specificity: 0.79)
SMART Domains Protein: ENSMUSP00000129300
Gene: ENSMUSG00000027079
AA Change: K325E

DomainStartEndE-ValueType
low complexity region 15 28 N/A INTRINSIC
Pfam:MobB 115 230 5.7e-24 PFAM
Pfam:Clp1 232 424 3e-62 PFAM
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.7%
  • 20x: 98.8%
Validation Efficiency 100% (54/54)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the Clp1 family. The encoded protein is a multifunctional kinase which is a component of the tRNA splicing endonuclease complex and a component of the pre-mRNA cleavage complex II. This protein is implicated in tRNA, mRNA, and siRNA maturation. Mutations in this gene are associated with pontocerebellar hypoplasia type 10 (PCH10). Alternatively splice transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]
PHENOTYPE: Mice homozygous for a kinase dead allele exhibit background sensitive lethality, motor neuron degeneration, defects in diaphragm innervation, progressive muscle weakness and impaired pre-tRNA processing. Mice homozygous for a globally targeted allele exhibit complete embryonic lethality. [provided by MGI curators]
Allele List at MGI

All alleles(6) : Gene trapped(6)
Other mutations in this stock
Total: 55 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
1700113H08Rik A G 10: 87,066,068 (GRCm39) T84A probably benign Het
Abca17 G A 17: 24,510,751 (GRCm39) S909L probably benign Het
Adamtsl3 A T 7: 82,169,929 (GRCm39) Y371F possibly damaging Het
Adcy9 A T 16: 4,236,228 (GRCm39) S394R probably damaging Het
Ahcyl1 T C 3: 107,575,011 (GRCm39) N444S probably damaging Het
Ahnak A C 19: 8,985,232 (GRCm39) D2172A probably damaging Het
Arhgef28 C T 13: 98,130,576 (GRCm39) D421N probably benign Het
Brd1 T A 15: 88,614,307 (GRCm39) E196V possibly damaging Het
Cabs1 A G 5: 88,128,300 (GRCm39) D317G probably damaging Het
Ccdc96 T C 5: 36,642,069 (GRCm39) I25T unknown Het
Clgn A G 8: 84,153,218 (GRCm39) R607G possibly damaging Het
Dcun1d1 A T 3: 35,975,185 (GRCm39) I52K probably benign Het
Dync2h1 G A 9: 7,176,911 (GRCm39) T16I probably damaging Het
Eif4a3l1 A T 6: 136,306,771 (GRCm39) I411F probably benign Het
Epb41l5 A G 1: 119,477,639 (GRCm39) F711L probably benign Het
Esr1 G A 10: 4,696,763 (GRCm39) W204* probably null Het
Fat2 A G 11: 55,172,127 (GRCm39) L2862P probably damaging Het
Frmd3 A G 4: 74,054,068 (GRCm39) E159G probably damaging Het
Gsto2 T A 19: 47,874,608 (GRCm39) C243S possibly damaging Het
Heg1 A G 16: 33,545,867 (GRCm39) H206R probably benign Het
Ifi203 A G 1: 173,750,133 (GRCm39) V862A probably benign Het
Ippk C T 13: 49,615,107 (GRCm39) H497Y probably benign Het
Irf5 A T 6: 29,531,317 (GRCm39) N61I possibly damaging Het
Iws1 G A 18: 32,213,213 (GRCm39) E214K possibly damaging Het
Kcnj12 C T 11: 60,960,673 (GRCm39) H324Y probably damaging Het
Kdm2a C T 19: 4,393,141 (GRCm39) D405N Het
Lars2 A G 9: 123,265,366 (GRCm39) Q474R probably benign Het
Lctl T C 9: 64,040,473 (GRCm39) F472S possibly damaging Het
Map4k2 T C 19: 6,401,223 (GRCm39) S590P probably benign Het
Mcf2l G T 8: 13,050,757 (GRCm39) L337F possibly damaging Het
Mvp A G 7: 126,595,435 (GRCm39) V225A probably damaging Het
Nfat5 T A 8: 108,065,910 (GRCm39) D241E probably damaging Het
Or6n2 T A 1: 173,897,021 (GRCm39) D52E probably benign Het
Pagr1a A T 7: 126,616,073 (GRCm39) H7Q probably damaging Het
Parp8 G T 13: 117,000,781 (GRCm39) Q787K probably damaging Het
Pcdhb2 C A 18: 37,429,369 (GRCm39) N90K probably damaging Het
Pde6h A G 6: 136,936,332 (GRCm39) K25R probably benign Het
Prr35 G A 17: 26,166,118 (GRCm39) Q390* probably null Het
Psd3 C A 8: 68,413,301 (GRCm39) A410S probably benign Het
Pus10 A G 11: 23,617,311 (GRCm39) N8S probably benign Het
Rnf115 T C 3: 96,695,994 (GRCm39) L260S probably damaging Het
Sdsl A T 5: 120,601,159 (GRCm39) Y38N probably benign Het
Sf1 A G 19: 6,415,694 (GRCm39) D11G probably damaging Het
Stxbp5l A G 16: 36,936,047 (GRCm39) Y1177H probably damaging Het
Taar2 G A 10: 23,816,900 (GRCm39) V147I probably benign Het
Tmed3 A T 9: 89,584,980 (GRCm39) F92I possibly damaging Het
Tmprss15 T C 16: 78,832,086 (GRCm39) T357A probably damaging Het
Trbv14 A T 6: 41,112,428 (GRCm39) D75V probably damaging Het
Vmn1r30 A G 6: 58,412,262 (GRCm39) V190A probably benign Het
Vmn2r115 A T 17: 23,578,482 (GRCm39) I652F probably benign Het
Vmn2r26 A T 6: 124,016,333 (GRCm39) M266L probably benign Het
Wdr17 T C 8: 55,143,057 (GRCm39) I198V probably benign Het
Wdr27 G A 17: 15,128,833 (GRCm39) A540V possibly damaging Het
Zfp26 A C 9: 20,349,447 (GRCm39) Y372* probably null Het
Zfp286 A G 11: 62,670,801 (GRCm39) V424A probably damaging Het
Other mutations in Clp1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02725:Clp1 APN 2 84,554,208 (GRCm39) missense probably benign 0.36
D4186:Clp1 UTSW 2 84,555,979 (GRCm39) missense probably benign 0.00
R0540:Clp1 UTSW 2 84,555,935 (GRCm39) missense possibly damaging 0.69
R0607:Clp1 UTSW 2 84,555,935 (GRCm39) missense possibly damaging 0.69
R1954:Clp1 UTSW 2 84,554,395 (GRCm39) missense probably damaging 1.00
R2908:Clp1 UTSW 2 84,554,488 (GRCm39) missense possibly damaging 0.89
R4769:Clp1 UTSW 2 84,556,219 (GRCm39) missense possibly damaging 0.53
R4949:Clp1 UTSW 2 84,554,086 (GRCm39) missense possibly damaging 0.58
R5568:Clp1 UTSW 2 84,556,322 (GRCm39) nonsense probably null
R7191:Clp1 UTSW 2 84,554,490 (GRCm39) nonsense probably null
R8341:Clp1 UTSW 2 84,554,117 (GRCm39) missense probably damaging 0.98
R9055:Clp1 UTSW 2 84,554,266 (GRCm39) missense probably damaging 1.00
R9220:Clp1 UTSW 2 84,554,076 (GRCm39) missense probably damaging 1.00
R9366:Clp1 UTSW 2 84,556,473 (GRCm39) missense probably benign
R9768:Clp1 UTSW 2 84,556,477 (GRCm39) start codon destroyed probably null 0.86
Z1177:Clp1 UTSW 2 84,556,307 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- TTGGTGTTCCACATCCACACTG -3'
(R):5'- CGAATTGAAAAGGGACCTGCC -3'

Sequencing Primer
(F):5'- TGGTCACAACAATGAATCCAGC -3'
(R):5'- GAAAAGGGACCTGCCTCATTTTG -3'
Posted On 2022-04-18