Incidental Mutation 'R9220:Clp1'
ID 699388
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 # R9220 (G1)
Quality Score 225.009
Status Not validated
Chromosome 2
Chromosomal Location 84553466-84557631 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 84554076 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Histidine to Glutamine at position 364 (H364Q)
Ref Sequence ENSEMBL: ENSMUSP00000028475 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028475] [ENSMUST00000165219]
AlphaFold Q99LI9
Predicted Effect probably damaging
Transcript: ENSMUST00000028475
AA Change: H364Q

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000028475
Gene: ENSMUSG00000027079
AA Change: H364Q

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 damaging
Transcript: ENSMUST00000165219
AA Change: H364Q

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)
SMART Domains Protein: ENSMUSP00000129300
Gene: ENSMUSG00000027079
AA Change: H364Q

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: 100.0%
  • 10x: 99.9%
  • 20x: 99.7%
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acte1 G T 7: 143,434,902 (GRCm39) probably null Het
Afg3l2 T G 18: 67,562,266 (GRCm39) I270L probably benign Het
Akap6 A T 12: 53,187,232 (GRCm39) I1549F possibly damaging Het
Ank2 T C 3: 126,737,086 (GRCm39) T2933A unknown Het
Atp1a3 C A 7: 24,696,625 (GRCm39) E309* probably null Het
B4galt2 T C 4: 117,734,399 (GRCm39) Y250C probably damaging Het
Bcl2l13 C A 6: 120,847,735 (GRCm39) T129K possibly damaging Het
Bltp3b A T 10: 89,626,457 (GRCm39) T384S probably benign Het
Ddx27 T C 2: 166,871,433 (GRCm39) V510A probably benign Het
Dicer1 A G 12: 104,679,415 (GRCm39) C521R probably damaging Het
Dnah10 A T 5: 124,871,437 (GRCm39) I2486F probably benign Het
Eml1 C A 12: 108,480,702 (GRCm39) C389* probably null Het
Fabp6 C T 11: 43,489,572 (GRCm39) G23D probably benign Het
Fam3b A T 16: 97,302,111 (GRCm39) S38T probably benign Het
Fsd1l A T 4: 53,679,799 (GRCm39) K166* probably null Het
Galc A G 12: 98,220,523 (GRCm39) S115P probably damaging Het
Gpn1 G A 5: 31,664,884 (GRCm39) A303T probably benign Het
Grid2 A T 6: 63,885,888 (GRCm39) S95C probably damaging Het
Helz T A 11: 107,560,873 (GRCm39) S1312T probably benign Het
Matn2 T C 15: 34,410,325 (GRCm39) F506L possibly damaging Het
Mcemp1 A G 8: 3,717,512 (GRCm39) S148G probably benign Het
Minar1 T A 9: 89,484,398 (GRCm39) D333V probably damaging Het
Ndrg1 A G 15: 66,805,711 (GRCm39) probably null Het
Nlrp4a A T 7: 26,149,523 (GRCm39) N377Y probably damaging Het
Nox4 C T 7: 86,970,774 (GRCm39) T217I probably benign Het
Or7g21 T C 9: 19,033,193 (GRCm39) F311S possibly damaging Het
Or8b52 A T 9: 38,576,803 (GRCm39) Y112* probably null Het
Phf8-ps T C 17: 33,286,494 (GRCm39) I103V probably benign Het
Plekhd1 T A 12: 80,768,726 (GRCm39) F403Y possibly damaging Het
Plekhg1 T C 10: 3,913,805 (GRCm39) S1231P Het
Plekhg3 T A 12: 76,618,839 (GRCm39) M497K probably benign Het
Rpap1 T C 2: 119,604,669 (GRCm39) H413R probably damaging Het
Rragd A G 4: 32,995,924 (GRCm39) T90A probably damaging Het
Septin9 T C 11: 117,242,396 (GRCm39) M286T probably benign Het
Shpk GACCTTAGCCAGAAGGAGCCTTAGTTCATCAA GA 11: 73,113,996 (GRCm39) probably null Het
Slc22a2 T A 17: 12,838,757 (GRCm39) D528E probably benign Het
Slirp G A 12: 87,494,376 (GRCm39) R47K probably benign Het
Sncg T C 14: 34,096,474 (GRCm39) T22A possibly damaging Het
Tnfrsf21 A G 17: 43,398,801 (GRCm39) S636G probably damaging Het
Unc80 T G 1: 66,546,534 (GRCm39) S535R probably damaging Het
Vmn1r149 A T 7: 22,137,378 (GRCm39) S93T probably benign Het
Vps13d A G 4: 144,783,058 (GRCm39) Y3957H Het
Wdr35 T A 12: 9,036,000 (GRCm39) V257E possibly damaging Het
Wscd1 A G 11: 71,662,750 (GRCm39) T264A probably benign Het
Zfp266 G A 9: 20,413,337 (GRCm39) Q108* probably null Het
Zfp62 T A 11: 49,106,075 (GRCm39) S55R 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
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
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'- ACCGGATATCCATGATGAGAAG -3'
(R):5'- GAACGTTCCAAGGACTTCCG -3'

Sequencing Primer
(F):5'- GAAAGTTCTTAGGCAATGGGC -3'
(R):5'- CGGGAATGTAGAGATGAACGTATCC -3'
Posted On 2022-02-07