Incidental Mutation 'R1870:Ccdc40'
ID 210678
Institutional Source Beutler Lab
Gene Symbol Ccdc40
Ensembl Gene ENSMUSG00000039963
Gene Name coiled-coil domain containing 40
Synonyms B930008I02Rik
MMRRC Submission 039892-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.174) question?
Stock # R1870 (G1)
Quality Score 215
Status Validated
Chromosome 11
Chromosomal Location 119119398-119156064 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 119150730 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 1011 (M1011T)
Ref Sequence ENSEMBL: ENSMUSP00000039463 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000035935] [ENSMUST00000053440]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000035935
AA Change: M1011T

PolyPhen 2 Score 0.807 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000039463
Gene: ENSMUSG00000039963
AA Change: M1011T

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 possibly damaging
Transcript: ENSMUST00000053440
AA Change: M1081T

PolyPhen 2 Score 0.637 (Sensitivity: 0.87; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000062198
Gene: ENSMUSG00000039963
AA Change: M1081T

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: ENSMUST00000125724
Predicted Effect noncoding transcript
Transcript: ENSMUST00000126652
Predicted Effect noncoding transcript
Transcript: ENSMUST00000133788
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155683
Meta Mutation Damage Score 0.1368 question?
Coding Region Coverage
  • 1x: 97.3%
  • 3x: 96.7%
  • 10x: 95.1%
  • 20x: 92.1%
Validation Efficiency 97% (96/99)
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: 89 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 A T 11: 9,242,134 (GRCm39) E1332D probably benign Het
Abca5 C A 11: 110,220,043 (GRCm39) V8L probably benign Het
Abcc8 C T 7: 45,773,339 (GRCm39) E797K probably benign Het
Acd C A 8: 106,425,039 (GRCm39) probably null Het
Adam34l A T 8: 44,078,132 (GRCm39) Y697* probably null Het
Adamts12 T C 15: 11,311,240 (GRCm39) S1166P probably benign Het
Alox12b T C 11: 69,049,199 (GRCm39) Y83H possibly damaging Het
Antxr2 A T 5: 98,178,297 (GRCm39) S38T probably damaging Het
Aox1 A G 1: 58,115,262 (GRCm39) E749G probably damaging Het
Arpc1a T A 5: 145,043,901 (GRCm39) C344S possibly damaging Het
Bcan T C 3: 87,902,908 (GRCm39) Y290C probably damaging Het
Bod1l G A 5: 41,991,018 (GRCm39) S179F possibly damaging Het
Catsper3 A C 13: 55,953,561 (GRCm39) D224A probably damaging Het
Ccar2 A G 14: 70,377,946 (GRCm39) S680P probably damaging Het
Ccdc18 A G 5: 108,368,703 (GRCm39) H1275R possibly damaging Het
Cfap46 T A 7: 139,263,386 (GRCm39) D17V probably damaging Het
Csn1s2a T C 5: 87,926,058 (GRCm39) F45L probably benign Het
Cwf19l2 T G 9: 3,458,802 (GRCm39) N750K possibly damaging Het
Cyb5r4 A G 9: 86,922,462 (GRCm39) D157G probably benign Het
D130040H23Rik T A 8: 69,755,354 (GRCm39) I253N probably benign Het
Dennd4a C T 9: 64,804,516 (GRCm39) A1285V probably benign Het
Dlat A G 9: 50,548,874 (GRCm39) S561P probably damaging Het
Dlgap2 T A 8: 14,823,347 (GRCm39) V522E probably damaging Het
Dnah5 T A 15: 28,331,859 (GRCm39) Y2148* probably null Het
Dnase2a T C 8: 85,635,392 (GRCm39) probably benign Het
Elapor2 A G 5: 9,468,007 (GRCm39) E225G probably damaging Het
Fam83f T C 15: 80,574,113 (GRCm39) probably benign Het
Firrm G A 1: 163,792,363 (GRCm39) L545F probably damaging Het
Foxi1 A T 11: 34,157,937 (GRCm39) N29K possibly damaging Het
Galk2 T C 2: 125,817,183 (GRCm39) L324P probably benign Het
Gdpd4 G A 7: 97,622,162 (GRCm39) V214I probably benign Het
Gfra3 C T 18: 34,844,373 (GRCm39) A56T probably damaging Het
Glyctk A G 9: 106,032,547 (GRCm39) S489P probably damaging Het
Izumo4 A T 10: 80,539,569 (GRCm39) I135F probably damaging Het
Krt87 T A 15: 101,385,071 (GRCm39) T342S probably benign Het
L1td1 T A 4: 98,625,714 (GRCm39) D636E possibly damaging Het
Letm2 A G 8: 26,086,460 (GRCm39) probably benign Het
Lpin1 A G 12: 16,591,744 (GRCm39) F828L probably damaging Het
Lrrc37 T C 11: 103,511,431 (GRCm39) D179G unknown Het
Mdn1 T A 4: 32,763,339 (GRCm39) D5146E probably damaging Het
Megf10 T A 18: 57,324,257 (GRCm39) Y99* probably null Het
Men1 A G 19: 6,387,660 (GRCm39) D285G probably damaging Het
Mertk T G 2: 128,643,116 (GRCm39) D838E probably benign Het
Mta1 T C 12: 113,091,694 (GRCm39) S266P possibly damaging Het
Mta3 G A 17: 84,089,397 (GRCm39) V320M probably damaging Het
Nlrp9c G A 7: 26,084,245 (GRCm39) Q445* probably null Het
Or2m12 A T 16: 19,105,357 (GRCm39) N45K probably damaging Het
Or51e1 T C 7: 102,358,961 (GRCm39) I165T possibly damaging Het
Or8b38 A T 9: 37,972,646 (GRCm39) K10I probably benign Het
Or8d6 T G 9: 39,854,117 (GRCm39) I187R probably damaging Het
Pbrm1 T A 14: 30,828,132 (GRCm39) L1320I probably damaging Het
Pdzd2 G T 15: 12,457,972 (GRCm39) T297K probably damaging Het
Pfas T C 11: 68,882,795 (GRCm39) D782G probably damaging Het
Pik3c3 T C 18: 30,426,185 (GRCm39) probably null Het
Pira2 T C 7: 3,847,452 (GRCm39) N79S probably damaging Het
Pkdrej G T 15: 85,700,632 (GRCm39) T1768K probably damaging Het
Plcb3 T C 19: 6,940,353 (GRCm39) I439V probably benign Het
Pold4 T A 19: 4,282,593 (GRCm39) Y58* probably null Het
Ppef2 T G 5: 92,398,371 (GRCm39) Q49P probably damaging Het
Ralgapa1 T A 12: 55,723,817 (GRCm39) I2026F possibly damaging Het
Rest T A 5: 77,416,209 (GRCm39) V141E possibly damaging Het
Rnf139 T C 15: 58,771,202 (GRCm39) V409A probably benign Het
Rnpc3 T C 3: 113,404,704 (GRCm39) probably benign Het
S100a10 A T 3: 93,468,377 (GRCm39) E36V probably benign Het
S1pr3 A C 13: 51,573,952 (GRCm39) K378Q probably benign Het
Scaper T A 9: 55,593,222 (GRCm39) I472F probably damaging Het
Sgcg G A 14: 61,477,896 (GRCm39) probably benign Het
Shank1 A T 7: 43,991,539 (GRCm39) R69* probably null Het
Shoc1 G A 4: 59,054,142 (GRCm39) probably benign Het
Siglecf A G 7: 43,004,967 (GRCm39) N399S probably benign Het
Slc25a54 T A 3: 108,987,932 (GRCm39) Y24* probably null Het
Slc29a4 T C 5: 142,707,243 (GRCm39) *529R probably null Het
Slc41a2 G A 10: 83,137,029 (GRCm39) Q293* probably null Het
Slc4a7 T C 14: 14,737,509 (GRCm38) probably null Het
Slfn9 G T 11: 82,872,402 (GRCm39) T778N probably benign Het
Ssr2 T C 3: 88,483,949 (GRCm39) probably benign Het
Tecrl T A 5: 83,502,706 (GRCm39) T33S probably benign Het
Tnfrsf9 T A 4: 151,018,804 (GRCm39) C158* probably null Het
Tradd T C 8: 105,985,792 (GRCm39) E253G possibly damaging Het
Usp34 A G 11: 23,314,479 (GRCm39) H807R probably benign Het
Vmn2r129 G T 4: 156,686,692 (GRCm39) noncoding transcript Het
Vmn2r27 T C 6: 124,201,170 (GRCm39) I262M probably benign Het
Vps13a A G 19: 16,737,316 (GRCm39) V91A probably damaging Het
Vwf C T 6: 125,619,902 (GRCm39) R1527C probably damaging Het
Wwc1 C T 11: 35,752,772 (GRCm39) G763D probably damaging Het
Zfp526 T G 7: 24,924,594 (GRCm39) D284E possibly damaging Het
Zfp646 T C 7: 127,483,021 (GRCm39) F1733L possibly damaging Het
Zfp90 A G 8: 107,145,755 (GRCm39) H29R probably benign Het
Zkscan4 A G 13: 21,668,104 (GRCm39) E185G 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
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
R4663:Ccdc40 UTSW 11 119,122,332 (GRCm39) missense probably benign 0.01
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'- CCTTCTCCATCAATGTGCACAG -3'
(R):5'- CAGGAACACATTGCTCACGTC -3'

Sequencing Primer
(F):5'- GTCCCCCAGACTCCTTGAAG -3'
(R):5'- ACATTGCTCACGTCACTGGG -3'
Posted On 2014-06-30