Incidental Mutation 'R4769:Clp1'
ID 366314
Institutional Source Beutler Lab
Gene Symbol Clp1
Ensembl Gene ENSMUSG00000027079
Gene Name CLP1, cleavage and polyadenylation factor I subunit
Synonyms
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4769 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 84553466-84557631 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 84556219 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Glycine at position 87 (D87G)
Ref Sequence ENSEMBL: ENSMUSP00000129300 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028475] [ENSMUST00000165219]
AlphaFold Q99LI9
Predicted Effect possibly damaging
Transcript: ENSMUST00000028475
AA Change: D87G

PolyPhen 2 Score 0.534 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000028475
Gene: ENSMUSG00000027079
AA Change: D87G

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 noncoding transcript
Transcript: ENSMUST00000138231
Predicted Effect possibly damaging
Transcript: ENSMUST00000165219
AA Change: D87G

PolyPhen 2 Score 0.534 (Sensitivity: 0.88; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000129300
Gene: ENSMUSG00000027079
AA Change: D87G

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: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.8%
Validation Efficiency
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: 50 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
3425401B19Rik A C 14: 32,382,174 (GRCm39) S1264A probably benign Het
Adamts13 T G 2: 26,898,723 (GRCm39) Y1361* probably null Het
Ahrr A T 13: 74,362,331 (GRCm39) D389E probably damaging Het
Alx3 T C 3: 107,508,007 (GRCm39) F172S probably damaging Het
Antxrl A G 14: 33,795,027 (GRCm39) H485R possibly damaging Het
Aox4 A G 1: 58,298,307 (GRCm39) D1091G probably null Het
Btbd1 T A 7: 81,455,558 (GRCm39) Q271L probably benign Het
Cd209c A T 8: 3,994,953 (GRCm39) N70K probably benign Het
Cdc14a C T 3: 116,088,399 (GRCm39) probably null Het
Cenpe A G 3: 134,953,912 (GRCm39) M1641V probably benign Het
Clec2e G A 6: 129,077,790 (GRCm39) T16I probably benign Het
Dpy19l1 A T 9: 24,337,444 (GRCm39) F517I probably damaging Het
Dzip3 T C 16: 48,758,837 (GRCm39) N646S probably damaging Het
Ephx1 T A 1: 180,823,543 (GRCm39) Y188F possibly damaging Het
Etfa A T 9: 55,403,051 (GRCm39) H81Q possibly damaging Het
Gigyf2 T A 1: 87,368,571 (GRCm39) F1084I probably damaging Het
Heatr3 T C 8: 88,868,411 (GRCm39) probably null Het
Ift81 G T 5: 122,732,656 (GRCm39) H293N probably benign Het
Igkv9-120 G T 6: 68,027,351 (GRCm39) R88S possibly damaging Het
Il6 T G 5: 30,223,076 (GRCm39) L114* probably null Het
Ism2 A T 12: 87,346,355 (GRCm39) M42K probably benign Het
Lhx5 A G 5: 120,574,503 (GRCm39) E269G probably benign Het
Marveld1 T G 19: 42,136,434 (GRCm39) M116R possibly damaging Het
Micall2 A G 5: 139,692,641 (GRCm39) S911P probably damaging Het
Mier1 G A 4: 102,997,417 (GRCm39) R195H probably benign Het
Muc2 T A 7: 141,286,260 (GRCm39) probably null Het
Mybbp1a A G 11: 72,336,466 (GRCm39) K486R probably damaging Het
Ncapd2 A C 6: 125,162,708 (GRCm39) L179R probably damaging Het
Nos1 C T 5: 118,081,310 (GRCm39) Q1171* probably null Het
Nrg1 T A 8: 32,408,000 (GRCm39) I78F probably damaging Het
Or5d36 T G 2: 87,901,073 (GRCm39) T218P probably benign Het
Or6y1 T G 1: 174,276,524 (GRCm39) F112V possibly damaging Het
Plek2 C T 12: 78,953,664 (GRCm39) probably null Het
Plod2 A G 9: 92,477,325 (GRCm39) H339R probably damaging Het
Pold1 C T 7: 44,184,495 (GRCm39) C835Y probably damaging Het
Polr1a A G 6: 71,927,852 (GRCm39) I868V probably benign Het
Prss54 C A 8: 96,286,003 (GRCm39) V357L probably benign Het
Rbbp8 T A 18: 11,855,727 (GRCm39) S625T probably damaging Het
Rgs1 A T 1: 144,123,667 (GRCm39) L86Q probably damaging Het
Ripk4 T A 16: 97,545,262 (GRCm39) N462Y probably damaging Het
Rsf1 C T 7: 97,325,429 (GRCm39) L1011F probably damaging Het
Slc19a3 G A 1: 82,997,062 (GRCm39) T382I probably damaging Het
Slc9a2 G A 1: 40,765,534 (GRCm39) R308Q probably damaging Het
Top2b T A 14: 16,398,991 (GRCm38) L537Q probably damaging Het
Trim45 C A 3: 100,839,050 (GRCm39) probably benign Het
Umodl1 G T 17: 31,202,976 (GRCm39) R443M possibly damaging Het
Vmn1r11 G A 6: 57,114,597 (GRCm39) R87K probably damaging Het
Vmn1r78 T A 7: 11,886,725 (GRCm39) I112N probably damaging Het
Zeb2 T G 2: 44,886,447 (GRCm39) E825A probably damaging Het
Zfp930 A T 8: 69,679,344 (GRCm39) I50F probably benign 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
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
R9351:Clp1 UTSW 2 84,554,195 (GRCm39) missense probably benign 0.01
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'- TGGCCTACATCTAACTCCACG -3'
(R):5'- AACAGAGCTTCGATTTGAGGTGG -3'

Sequencing Primer
(F):5'- GTAAGTAGGACGGCGGCC -3'
(R):5'- GAGGCCTCTCAATCGGTTCAG -3'
Posted On 2015-12-21