Incidental Mutation 'R5319:Cdk5rap1'
ID 405966
Institutional Source Beutler Lab
Gene Symbol Cdk5rap1
Ensembl Gene ENSMUSG00000027487
Gene Name CDK5 regulatory subunit associated protein 1
Synonyms 2310066P17Rik
MMRRC Submission 042902-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.366) question?
Stock # R5319 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 154177300-154214930 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 154177489 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Serine at position 577 (T577S)
Ref Sequence ENSEMBL: ENSMUSP00000105353 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028990] [ENSMUST00000109731]
AlphaFold Q8BTW8
Predicted Effect possibly damaging
Transcript: ENSMUST00000028990
AA Change: T577S

PolyPhen 2 Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000028990
Gene: ENSMUSG00000027487
AA Change: T577S

DomainStartEndE-ValueType
Pfam:UPF0004 100 203 3.2e-31 PFAM
Elp3 247 486 4.83e-52 SMART
Pfam:TRAM 500 574 1.2e-11 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000109731
AA Change: T577S

PolyPhen 2 Score 0.615 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000105353
Gene: ENSMUSG00000027487
AA Change: T577S

DomainStartEndE-ValueType
Pfam:UPF0004 100 203 1.1e-31 PFAM
Elp3 247 486 4.83e-52 SMART
Pfam:TRAM 500 574 1e-12 PFAM
Meta Mutation Damage Score 0.1348 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.5%
  • 20x: 95.8%
Validation Efficiency 95% (69/73)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a regulator of cyclin-dependent kinase 5 activity. This protein has also been reported to modify RNA by adding a methylthio-group and may thus have a dual function as an RNA methylthiotransferase and as an inhibitor of cyclin-dependent kinase 5 activity. Alternative splicing results in multiple transcript variants that encode different isoforms. [provided by RefSeq, May 2013]
PHENOTYPE: Mice homozygous for a null allele show deficient mitochondrial tRNA modification, reduced mitochondrial protein synthesis, defects in oxidative phosphorylation, high susceptibility to stress-induced mitochondrial remodeling, and accelerated myopathy and cardiac dysfunction under stressed conditions. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 62 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930449I24Rik T C 5: 146,441,506 (GRCm39) S218P probably benign Het
Ahctf1 A C 1: 179,596,615 (GRCm39) S121A probably damaging Het
Anpep C T 7: 79,491,479 (GRCm39) R174H probably benign Het
Arhgef18 T C 8: 3,435,010 (GRCm39) probably null Het
Becn1 A G 11: 101,179,629 (GRCm39) probably benign Het
Cabin1 T C 10: 75,561,549 (GRCm39) Y984C probably damaging Het
Cacna2d4 G T 6: 119,324,213 (GRCm39) probably null Het
Ccdc14 T G 16: 34,543,542 (GRCm39) N633K probably damaging Het
Clca4b T C 3: 144,630,940 (GRCm39) R307G possibly damaging Het
Colgalt2 A G 1: 152,360,620 (GRCm39) Q219R possibly damaging Het
Cops3 A T 11: 59,718,762 (GRCm39) D177E possibly damaging Het
Cyp2d9 T C 15: 82,338,256 (GRCm39) Y127H probably damaging Het
Dnajc11 A G 4: 152,052,983 (GRCm39) T98A probably damaging Het
Dst T C 1: 34,265,058 (GRCm39) S4757P possibly damaging Het
Dvl2 C T 11: 69,898,957 (GRCm39) T448I possibly damaging Het
E230016K23Rik T G 11: 83,512,496 (GRCm39) noncoding transcript Het
Efl1 G T 7: 82,323,714 (GRCm39) D219Y probably damaging Het
Epha10 T A 4: 124,807,793 (GRCm39) probably benign Het
Fbxw22 T A 9: 109,213,015 (GRCm39) T311S possibly damaging Het
Folr1 T A 7: 101,513,184 (GRCm39) D37V probably damaging Het
Fshb T A 2: 106,889,224 (GRCm39) I27F probably damaging Het
Gm8521 A T Y: 3,859,335 (GRCm39) noncoding transcript Het
Gpr45 T C 1: 43,071,998 (GRCm39) S214P probably damaging Het
Hgf G A 5: 16,771,860 (GRCm39) probably null Het
Hs6st1 T C 1: 36,143,259 (GRCm39) V398A probably benign Het
Ighmbp2 A G 19: 3,321,646 (GRCm39) V371A probably damaging Het
Kif18a T A 2: 109,148,370 (GRCm39) N621K probably benign Het
Lama5 A G 2: 179,822,911 (GRCm39) F2785S probably damaging Het
Lcor G A 19: 41,574,791 (GRCm39) G1182D probably damaging Het
Lrriq3 T C 3: 154,835,108 (GRCm39) I281T possibly damaging Het
Macf1 C T 4: 123,367,229 (GRCm39) A2511T probably damaging Het
Mark4 T C 7: 19,170,886 (GRCm39) D328G possibly damaging Het
Myo1c G A 11: 75,552,852 (GRCm39) E434K possibly damaging Het
Nfe2l1 A G 11: 96,710,205 (GRCm39) S387P probably damaging Het
Nr1d2 A G 14: 18,215,197 (GRCm38) S272P probably benign Het
Nsrp1 T C 11: 76,940,293 (GRCm39) H104R probably damaging Het
Odf1 T A 15: 38,219,863 (GRCm39) S64T probably benign Het
Or2aa1 A T 11: 59,480,477 (GRCm39) V146E probably damaging Het
Or4c106 T A 2: 88,683,122 (GRCm39) I276K probably damaging Het
Or7g25 C T 9: 19,160,329 (GRCm39) R122H possibly damaging Het
Pde4b C A 4: 102,278,985 (GRCm39) probably benign Het
Phox2a C T 7: 101,470,057 (GRCm39) T96M probably damaging Het
Plg A G 17: 12,622,114 (GRCm39) E478G possibly damaging Het
Polr3a T C 14: 24,505,009 (GRCm39) I1084V possibly damaging Het
Ppp1r12c T A 7: 4,486,983 (GRCm39) T517S probably benign Het
Ptk7 C T 17: 46,883,603 (GRCm39) V821M probably damaging Het
Ptpn6 C T 6: 124,709,913 (GRCm39) V2M probably benign Het
Rgl2 T C 17: 34,152,529 (GRCm39) V380A probably benign Het
Rpl13a-ps1 A G 19: 50,018,591 (GRCm39) V195A possibly damaging Het
Rsph1 C A 17: 31,492,351 (GRCm39) V72F probably benign Het
Sh3bp4 T C 1: 89,073,072 (GRCm39) V640A probably benign Het
Simc1 T A 13: 54,672,795 (GRCm39) V381E probably benign Het
Slc15a3 A T 19: 10,833,296 (GRCm39) T438S probably damaging Het
Slc5a4b C T 10: 75,898,233 (GRCm39) V494M probably benign Het
Sos2 C A 12: 69,674,058 (GRCm39) R335L probably benign Het
Trp53i13 A T 11: 77,399,566 (GRCm39) N254K probably damaging Het
Trpc6 A G 9: 8,609,922 (GRCm39) Y130C probably damaging Het
Trpv1 A G 11: 73,130,415 (GRCm39) I174V probably damaging Het
Tsnax T A 8: 125,742,458 (GRCm39) D62E probably damaging Het
Vezt T A 10: 93,806,193 (GRCm39) E739D probably benign Het
Vmn1r59 T A 7: 5,457,209 (GRCm39) I184F probably damaging Het
Yeats2 T C 16: 20,005,175 (GRCm39) V385A probably benign Het
Other mutations in Cdk5rap1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01778:Cdk5rap1 APN 2 154,207,956 (GRCm39) missense probably damaging 1.00
IGL02162:Cdk5rap1 APN 2 154,177,489 (GRCm39) missense probably damaging 0.98
IGL02626:Cdk5rap1 APN 2 154,207,880 (GRCm39) critical splice donor site probably null
IGL03278:Cdk5rap1 APN 2 154,212,622 (GRCm39) missense probably benign 0.00
R1052:Cdk5rap1 UTSW 2 154,202,519 (GRCm39) missense possibly damaging 0.96
R1333:Cdk5rap1 UTSW 2 154,202,574 (GRCm39) missense probably damaging 0.97
R1552:Cdk5rap1 UTSW 2 154,212,615 (GRCm39) missense probably benign 0.00
R1553:Cdk5rap1 UTSW 2 154,194,171 (GRCm39) missense probably damaging 1.00
R2107:Cdk5rap1 UTSW 2 154,195,166 (GRCm39) missense probably benign 0.22
R3946:Cdk5rap1 UTSW 2 154,190,636 (GRCm39) missense probably damaging 1.00
R4126:Cdk5rap1 UTSW 2 154,210,815 (GRCm39) missense probably damaging 1.00
R4715:Cdk5rap1 UTSW 2 154,203,755 (GRCm39) makesense probably null
R4865:Cdk5rap1 UTSW 2 154,212,876 (GRCm39) critical splice acceptor site probably null
R4866:Cdk5rap1 UTSW 2 154,212,876 (GRCm39) critical splice acceptor site probably null
R4867:Cdk5rap1 UTSW 2 154,212,876 (GRCm39) critical splice acceptor site probably null
R4946:Cdk5rap1 UTSW 2 154,210,794 (GRCm39) missense possibly damaging 0.91
R5087:Cdk5rap1 UTSW 2 154,184,315 (GRCm39) missense probably damaging 1.00
R5383:Cdk5rap1 UTSW 2 154,192,755 (GRCm39) missense possibly damaging 0.78
R5582:Cdk5rap1 UTSW 2 154,187,894 (GRCm39) missense probably benign 0.01
R5780:Cdk5rap1 UTSW 2 154,187,788 (GRCm39) frame shift probably null
R6262:Cdk5rap1 UTSW 2 154,212,606 (GRCm39) missense probably benign 0.04
R6274:Cdk5rap1 UTSW 2 154,210,161 (GRCm39) missense probably damaging 0.99
R7263:Cdk5rap1 UTSW 2 154,202,652 (GRCm39) missense probably benign 0.12
R7388:Cdk5rap1 UTSW 2 154,202,595 (GRCm39) missense probably damaging 1.00
R7650:Cdk5rap1 UTSW 2 154,196,036 (GRCm39) missense probably benign 0.01
R8424:Cdk5rap1 UTSW 2 154,187,932 (GRCm39) missense probably damaging 1.00
R8694:Cdk5rap1 UTSW 2 154,195,148 (GRCm39) nonsense probably null
R9295:Cdk5rap1 UTSW 2 154,194,186 (GRCm39) missense probably damaging 1.00
R9413:Cdk5rap1 UTSW 2 154,207,880 (GRCm39) critical splice donor site probably null
R9453:Cdk5rap1 UTSW 2 154,190,585 (GRCm39) missense probably damaging 1.00
R9466:Cdk5rap1 UTSW 2 154,192,756 (GRCm39) missense possibly damaging 0.64
Predicted Primers PCR Primer
(F):5'- TGCTGAGAAGCATCCAACAG -3'
(R):5'- ACTGATCACTGCAGTTGGGC -3'

Sequencing Primer
(F):5'- CTGAGAAGCATCCAACAGAGAGAC -3'
(R):5'- ACTGCAGTTGGGCCTTCC -3'
Posted On 2016-07-22