Incidental Mutation 'R4663:Ccdc40'
ID 353033
Institutional Source Beutler Lab
Gene Symbol Ccdc40
Ensembl Gene ENSMUSG00000039963
Gene Name coiled-coil domain containing 40
Synonyms B930008I02Rik
MMRRC Submission 041921-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.174) question?
Stock # R4663 (G1)
Quality Score 225
Status Not validated
Chromosome 11
Chromosomal Location 119119398-119156064 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 119122332 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 45 (I45V)
Ref Sequence ENSEMBL: ENSMUSP00000062198 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035935] [ENSMUST00000036113] [ENSMUST00000053440] [ENSMUST00000207655]
AlphaFold no structure available at present
Predicted Effect probably benign
Transcript: ENSMUST00000035935
SMART Domains Protein: ENSMUSP00000039463
Gene: ENSMUSG00000039963

DomainStartEndE-ValueType
internal_repeat_1 7 48 1.25e-8 PROSPERO
internal_repeat_1 55 96 1.25e-8 PROSPERO
low complexity region 159 170 N/A INTRINSIC
low complexity region 208 232 N/A INTRINSIC
coiled coil region 349 371 N/A INTRINSIC
coiled coil region 423 447 N/A INTRINSIC
Blast:HisKA 450 519 3e-13 BLAST
Blast:HisKA 574 629 5e-8 BLAST
low complexity region 793 805 N/A INTRINSIC
Pfam:BRE1 830 928 4.2e-20 PFAM
coiled coil region 1044 1112 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000036113
SMART Domains Protein: ENSMUSP00000048516
Gene: ENSMUSG00000039976

DomainStartEndE-ValueType
low complexity region 17 30 N/A INTRINSIC
Blast:TBC 63 362 5e-75 BLAST
Blast:TBC 373 418 2e-13 BLAST
TBC 421 659 4.39e-43 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000053440
AA Change: I45V

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)
SMART Domains Protein: ENSMUSP00000062198
Gene: ENSMUSG00000039963
AA Change: I45V

DomainStartEndE-ValueType
low complexity region 5 27 N/A INTRINSIC
low complexity region 56 70 N/A INTRINSIC
internal_repeat_1 79 114 5.57e-8 PROSPERO
internal_repeat_1 111 150 5.57e-8 PROSPERO
low complexity region 229 240 N/A INTRINSIC
low complexity region 278 302 N/A INTRINSIC
coiled coil region 419 441 N/A INTRINSIC
coiled coil region 493 517 N/A INTRINSIC
Blast:HisKA 520 589 2e-13 BLAST
Blast:HisKA 644 699 4e-8 BLAST
low complexity region 863 875 N/A INTRINSIC
Pfam:BRE1 900 998 4e-20 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147037
Predicted Effect noncoding transcript
Transcript: ENSMUST00000150358
Predicted Effect probably benign
Transcript: ENSMUST00000207655
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
PHENOTYPE: Mice homozygous for an ENU-induced allele exhibit heterotaxia, hydrocephalus, short embryonic cilia, and postnatal lethality. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 72 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aqr A T 2: 113,992,147 (GRCm39) Y76* probably null Het
Armc5 C A 7: 127,837,717 (GRCm39) A140E probably benign Het
Auts2 T C 5: 131,468,476 (GRCm39) H947R probably damaging Het
Bag2 T C 1: 33,786,074 (GRCm39) T83A probably damaging Het
Bag4 C T 8: 26,259,516 (GRCm39) A228T probably benign Het
Bean1 A G 8: 104,937,799 (GRCm39) Y126C probably damaging Het
Cars1 T C 7: 143,129,697 (GRCm39) E330G probably damaging Het
Cd320 G A 17: 34,067,152 (GRCm39) G214R probably null Het
Ckm G A 7: 19,153,419 (GRCm39) V237M probably damaging Het
Cplane1 T C 15: 8,247,939 (GRCm39) V1496A probably benign Het
Cspg4 T C 9: 56,793,960 (GRCm39) V565A possibly damaging Het
Dnaaf10 T C 11: 17,182,853 (GRCm39) V338A probably benign Het
Eddm13 T G 7: 6,261,624 (GRCm39) I35S possibly damaging Het
Ephb6 A G 6: 41,594,799 (GRCm39) Y638C probably damaging Het
Fat2 G C 11: 55,187,039 (GRCm39) S1269* probably null Het
Fbxo3 T C 2: 103,883,820 (GRCm39) V348A probably damaging Het
Gas6 G A 8: 13,520,254 (GRCm39) P478L probably damaging Het
Herc1 T C 9: 66,340,660 (GRCm39) S1670P probably damaging Het
Hnrnpk C A 13: 58,542,331 (GRCm39) R281L probably damaging Het
Ifih1 C A 2: 62,439,563 (GRCm39) C488F probably benign Het
Ift172 T C 5: 31,441,559 (GRCm39) K192E probably benign Het
Ighv5-9 T A 12: 113,625,440 (GRCm39) Q101L probably benign Het
Igkv3-2 G T 6: 70,675,863 (GRCm39) M57I probably benign Het
Insyn2a A T 7: 134,500,877 (GRCm39) Y409* probably null Het
Itpr2 A G 6: 146,274,671 (GRCm39) F837S probably damaging Het
L3mbtl3 T C 10: 26,213,715 (GRCm39) Y237C unknown Het
Lats1 G A 10: 7,588,347 (GRCm39) C988Y probably damaging Het
Lgals3 T A 14: 47,619,079 (GRCm39) probably null Het
Lrrc3b G T 14: 15,358,220 (GRCm38) H129N probably benign Het
Lrriq1 T C 10: 102,899,273 (GRCm39) H1656R possibly damaging Het
Lypd6 T G 2: 50,063,623 (GRCm39) Y43* probably null Het
Mettl25b A G 3: 87,835,055 (GRCm39) S82P probably damaging Het
Mical2 A G 7: 111,927,884 (GRCm39) D674G possibly damaging Het
Msi1 G A 5: 115,588,334 (GRCm39) R284Q probably damaging Het
Mybpc2 T C 7: 44,155,066 (GRCm39) E947G probably damaging Het
Nat14 T A 7: 4,927,446 (GRCm39) L206Q probably damaging Het
Nup88 A T 11: 70,856,672 (GRCm39) probably null Het
Or11g27 A T 14: 50,771,061 (GRCm39) Y64F probably damaging Het
Or4k15 A G 14: 50,364,939 (GRCm39) R302G probably benign Het
Or8g19 A T 9: 39,056,145 (GRCm39) I250F probably damaging Het
Pdcl T C 2: 37,245,778 (GRCm39) E75G probably damaging Het
Phf14 A G 6: 11,953,421 (GRCm39) I387V possibly damaging Het
Phf3 G A 1: 30,860,296 (GRCm39) R845W probably damaging Het
Pm20d1 T C 1: 131,726,340 (GRCm39) I59T probably damaging Het
Prkd1 C T 12: 50,466,631 (GRCm39) probably null Het
Psmb2 T C 4: 126,571,558 (GRCm39) L4P probably damaging Het
Pttg1 T A 11: 43,315,677 (GRCm39) K46* probably null Het
Ryr2 T C 13: 11,764,395 (GRCm39) H1401R possibly damaging Het
Septin4 T A 11: 87,458,429 (GRCm39) Y268N probably damaging Het
Sh3d19 G A 3: 86,030,570 (GRCm39) D696N probably benign Het
Slc16a2 T C X: 102,751,585 (GRCm39) T274A probably benign Het
Slc26a6 G A 9: 108,735,106 (GRCm39) A335T probably damaging Het
Slc49a3 T C 5: 108,590,011 (GRCm39) M464V probably benign Het
Slc6a5 C A 7: 49,588,146 (GRCm39) Y493* probably null Het
Slf1 A T 13: 77,274,723 (GRCm39) S37R probably damaging Het
Smoc1 G A 12: 81,214,376 (GRCm39) G264S probably damaging Het
Snapc4 T C 2: 26,264,193 (GRCm39) E280G possibly damaging Het
Snx25 G A 8: 46,488,616 (GRCm39) T913M probably damaging Het
Snx7 T C 3: 117,594,528 (GRCm39) T408A probably benign Het
Spdya T A 17: 71,885,339 (GRCm39) S264R probably benign Het
Spg11 A T 2: 121,928,580 (GRCm39) probably null Het
Suz12 T A 11: 79,904,350 (GRCm39) L230Q probably damaging Het
Szt2 A G 4: 118,234,881 (GRCm39) probably benign Het
Tenm3 C A 8: 48,689,005 (GRCm39) R2194L probably damaging Het
Tmed8 T A 12: 87,221,005 (GRCm39) I194F probably damaging Het
Tmem79 T A 3: 88,240,751 (GRCm39) T66S probably damaging Het
Trappc1 T A 11: 69,216,337 (GRCm39) S118T probably benign Het
Ttn C T 2: 76,569,225 (GRCm39) V27223I probably benign Het
Ttn T C 2: 76,606,839 (GRCm39) T18024A probably damaging Het
Vmn2r15 C T 5: 109,441,940 (GRCm39) M164I probably benign Het
Vmn2r53 T A 7: 12,334,901 (GRCm39) Y253F probably benign Het
Zfand6 C T 7: 84,267,093 (GRCm39) R163H probably benign Het
Other mutations in Ccdc40
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01538:Ccdc40 APN 11 119,133,545 (GRCm39) missense possibly damaging 0.90
IGL01864:Ccdc40 APN 11 119,133,911 (GRCm39) missense probably benign 0.23
IGL01911:Ccdc40 APN 11 119,122,797 (GRCm39) splice site probably null
IGL02640:Ccdc40 APN 11 119,128,904 (GRCm39) missense probably benign 0.18
IGL03278:Ccdc40 APN 11 119,133,336 (GRCm39) missense probably damaging 1.00
IGL03054:Ccdc40 UTSW 11 119,154,027 (GRCm39) missense possibly damaging 0.69
PIT4151001:Ccdc40 UTSW 11 119,133,277 (GRCm39) missense probably damaging 1.00
R0139:Ccdc40 UTSW 11 119,155,125 (GRCm39) missense probably benign 0.00
R0140:Ccdc40 UTSW 11 119,155,125 (GRCm39) missense probably benign 0.00
R0415:Ccdc40 UTSW 11 119,122,944 (GRCm39) missense possibly damaging 0.92
R0617:Ccdc40 UTSW 11 119,133,630 (GRCm39) missense probably damaging 1.00
R1396:Ccdc40 UTSW 11 119,122,629 (GRCm39) missense possibly damaging 0.66
R1531:Ccdc40 UTSW 11 119,154,015 (GRCm39) missense probably benign 0.01
R1751:Ccdc40 UTSW 11 119,121,522 (GRCm39) critical splice donor site probably null
R1767:Ccdc40 UTSW 11 119,121,522 (GRCm39) critical splice donor site probably null
R1870:Ccdc40 UTSW 11 119,150,730 (GRCm39) missense possibly damaging 0.81
R1971:Ccdc40 UTSW 11 119,153,901 (GRCm39) splice site probably null
R2106:Ccdc40 UTSW 11 119,155,123 (GRCm39) missense probably damaging 1.00
R2370:Ccdc40 UTSW 11 119,153,943 (GRCm39) missense probably benign 0.00
R3421:Ccdc40 UTSW 11 119,125,605 (GRCm39) missense probably benign 0.02
R3746:Ccdc40 UTSW 11 119,155,252 (GRCm39) missense probably benign 0.26
R3749:Ccdc40 UTSW 11 119,155,252 (GRCm39) missense probably benign 0.26
R3871:Ccdc40 UTSW 11 119,155,107 (GRCm39) missense probably damaging 1.00
R4508:Ccdc40 UTSW 11 119,133,335 (GRCm39) missense probably damaging 0.98
R4613:Ccdc40 UTSW 11 119,122,358 (GRCm39) missense probably benign 0.09
R4787:Ccdc40 UTSW 11 119,144,447 (GRCm39) missense possibly damaging 0.74
R4867:Ccdc40 UTSW 11 119,122,614 (GRCm39) missense probably benign
R5237:Ccdc40 UTSW 11 119,150,802 (GRCm39) missense probably benign 0.00
R5661:Ccdc40 UTSW 11 119,128,753 (GRCm39) missense probably benign 0.13
R5678:Ccdc40 UTSW 11 119,122,398 (GRCm39) missense possibly damaging 0.61
R5805:Ccdc40 UTSW 11 119,136,906 (GRCm39) critical splice donor site probably null
R5830:Ccdc40 UTSW 11 119,133,572 (GRCm39) missense probably benign 0.00
R5895:Ccdc40 UTSW 11 119,144,229 (GRCm39) missense probably damaging 1.00
R5932:Ccdc40 UTSW 11 119,141,838 (GRCm39) missense probably damaging 0.98
R6034:Ccdc40 UTSW 11 119,133,898 (GRCm39) missense possibly damaging 0.70
R6034:Ccdc40 UTSW 11 119,133,898 (GRCm39) missense possibly damaging 0.70
R6109:Ccdc40 UTSW 11 119,122,804 (GRCm39) missense probably benign
R6166:Ccdc40 UTSW 11 119,122,827 (GRCm39) missense probably benign
R6336:Ccdc40 UTSW 11 119,122,819 (GRCm39) missense possibly damaging 0.82
R6569:Ccdc40 UTSW 11 119,133,560 (GRCm39) missense probably damaging 1.00
R6884:Ccdc40 UTSW 11 119,133,565 (GRCm39) missense possibly damaging 0.82
R7022:Ccdc40 UTSW 11 119,122,612 (GRCm39) missense possibly damaging 0.82
R7212:Ccdc40 UTSW 11 119,155,270 (GRCm39) missense probably damaging 0.99
R7472:Ccdc40 UTSW 11 119,153,974 (GRCm39) missense probably benign 0.30
R7522:Ccdc40 UTSW 11 119,123,047 (GRCm39) missense possibly damaging 0.73
R7888:Ccdc40 UTSW 11 119,119,967 (GRCm39) missense unknown
R8041:Ccdc40 UTSW 11 119,122,507 (GRCm39) missense possibly damaging 0.53
R8117:Ccdc40 UTSW 11 119,144,211 (GRCm39) missense probably benign 0.00
R8162:Ccdc40 UTSW 11 119,150,870 (GRCm39) critical splice donor site probably null
R8514:Ccdc40 UTSW 11 119,121,459 (GRCm39) missense unknown
R8725:Ccdc40 UTSW 11 119,155,323 (GRCm39) missense probably benign
R8727:Ccdc40 UTSW 11 119,155,323 (GRCm39) missense probably benign
R8799:Ccdc40 UTSW 11 119,155,292 (GRCm39) missense probably benign 0.00
R8877:Ccdc40 UTSW 11 119,153,992 (GRCm39) missense probably damaging 1.00
R9304:Ccdc40 UTSW 11 119,122,597 (GRCm39) missense probably benign 0.06
S24628:Ccdc40 UTSW 11 119,122,944 (GRCm39) missense possibly damaging 0.92
Z1176:Ccdc40 UTSW 11 119,142,834 (GRCm39) missense probably damaging 1.00
Z1177:Ccdc40 UTSW 11 119,145,224 (GRCm39) missense probably benign 0.16
Z1177:Ccdc40 UTSW 11 119,128,933 (GRCm39) missense probably damaging 0.96
Predicted Primers PCR Primer
(F):5'- CATGCTTGTAACACGTGCC -3'
(R):5'- TTCCACATCTGTGTCTGGAGC -3'

Sequencing Primer
(F):5'- GCTTGTAACACGTGCCTCTAGAAAG -3'
(R):5'- GAGCGGTCTCTCCAATGAATTC -3'
Posted On 2015-10-08