Incidental Mutation 'R5920:Ift56'
ID 461520
Institutional Source Beutler Lab
Gene Symbol Ift56
Ensembl Gene ENSMUSG00000056832
Gene Name intraflagellar transport 56
Synonyms hpy, hydrocephalic-polydactyl, 9430097H08Rik, hop, Ttc26
MMRRC Submission 044117-MU
Accession Numbers
Essential gene? Possibly essential (E-score: 0.578) question?
Stock # R5920 (G1)
Quality Score 225
Status Not validated
Chromosome 6
Chromosomal Location 38358404-38404582 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 38389005 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 430 (Y430C)
Ref Sequence ENSEMBL: ENSMUSP00000124369 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000159145] [ENSMUST00000162554]
AlphaFold Q8BS45
Predicted Effect probably benign
Transcript: ENSMUST00000159145
SMART Domains Protein: ENSMUSP00000124873
Gene: ENSMUSG00000056832

DomainStartEndE-ValueType
low complexity region 19 29 N/A INTRINSIC
Pfam:TPR_2 58 88 1.2e-5 PFAM
Pfam:TPR_8 58 91 1.7e-3 PFAM
Pfam:TPR_1 61 87 4.6e-4 PFAM
Pfam:TPR_11 63 113 4.9e-11 PFAM
Pfam:TPR_19 67 113 3.1e-7 PFAM
Pfam:TPR_8 89 113 2e-3 PFAM
Pfam:TPR_1 91 113 1.7e-4 PFAM
Pfam:TPR_2 91 113 2.4e-3 PFAM
Predicted Effect probably damaging
Transcript: ENSMUST00000162554
AA Change: Y430C

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000124369
Gene: ENSMUSG00000056832
AA Change: Y430C

DomainStartEndE-ValueType
low complexity region 19 29 N/A INTRINSIC
Pfam:TPR_2 58 88 2.7e-5 PFAM
Pfam:TPR_11 63 117 9e-9 PFAM
Pfam:TPR_9 157 227 9.2e-4 PFAM
Blast:TPR 359 392 9e-10 BLAST
Blast:TPR 461 494 8e-15 BLAST
Coding Region Coverage
  • 1x: 99.8%
  • 3x: 99.4%
  • 10x: 97.4%
  • 20x: 92.4%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for a spontaneous nonsense mutation exhibit partial prenatal lethality, a hopping gait, preaxial polydactyly, male sterility due to lack of sperm flagella, impaired hearing, and patterning defects that are typical of impaired Hedgehog signaling. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 42 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam18 T C 8: 25,164,091 (GRCm39) K31E probably damaging Het
Ak9 T A 10: 41,296,672 (GRCm39) C1473S probably benign Het
Aox1 T C 1: 58,088,631 (GRCm39) L139S probably damaging Het
Arhgap45 T A 10: 79,864,965 (GRCm39) V849D possibly damaging Het
Atp13a1 G A 8: 70,252,746 (GRCm39) E689K probably benign Het
Calcr G A 6: 3,722,994 (GRCm39) R11W probably damaging Het
Casd1 T A 6: 4,641,853 (GRCm39) L710Q probably null Het
Cenpc1 T A 5: 86,168,769 (GRCm39) T743S probably benign Het
Cfap43 A G 19: 47,749,335 (GRCm39) V1185A possibly damaging Het
Chd2 A G 7: 73,187,060 (GRCm39) L33P probably damaging Het
Col24a1 G T 3: 145,133,985 (GRCm39) G889C probably damaging Het
Cracdl T A 1: 37,677,062 (GRCm39) K40M probably damaging Het
Dbh T C 2: 27,067,243 (GRCm39) probably benign Het
Dcdc2c T C 12: 28,585,536 (GRCm39) I154V possibly damaging Het
Eif2b5 G T 16: 20,317,694 (GRCm39) A11S unknown Het
Frmd4a T G 2: 4,337,927 (GRCm39) N44K probably benign Het
Fsip2 C T 2: 82,818,852 (GRCm39) Q4862* probably null Het
Hectd4 C T 5: 121,446,334 (GRCm39) T1513I possibly damaging Het
Hspg2 A T 4: 137,281,093 (GRCm39) D3355V probably damaging Het
Il16 G A 7: 83,301,552 (GRCm39) T190I probably benign Het
Immt T A 6: 71,840,180 (GRCm39) V319D probably benign Het
Kdm2b G C 5: 123,018,359 (GRCm39) S989W probably damaging Het
Kmt2e A G 5: 23,704,440 (GRCm39) E1211G possibly damaging Het
Ktn1 G T 14: 47,961,481 (GRCm39) G1061* probably null Het
Mast3 T C 8: 71,240,577 (GRCm39) I287V probably benign Het
Mrgpre T A 7: 143,335,465 (GRCm39) T13S probably benign Het
Myoc C T 1: 162,467,128 (GRCm39) A99V probably benign Het
Or10a49 C A 7: 108,467,895 (GRCm39) M155I probably benign Het
Otulinl T A 15: 27,664,442 (GRCm39) R109S possibly damaging Het
Per3 G A 4: 151,096,907 (GRCm39) P873S probably benign Het
Phykpl A C 11: 51,493,622 (GRCm39) E453A probably benign Het
Pkd2l2 A T 18: 34,563,826 (GRCm39) I514L probably benign Het
Plcl2 G T 17: 50,915,703 (GRCm39) R904L probably damaging Het
Ptpn1 A G 2: 167,813,668 (GRCm39) D137G probably benign Het
Rasal3 G A 17: 32,614,143 (GRCm39) P571S probably damaging Het
Sdha A G 13: 74,475,044 (GRCm39) probably null Het
Tbc1d31 C A 15: 57,805,954 (GRCm39) Q439K probably benign Het
Ttc12 T C 9: 49,364,633 (GRCm39) D381G possibly damaging Het
Uaca T A 9: 60,776,885 (GRCm39) M424K probably benign Het
Usp33 G T 3: 152,080,320 (GRCm39) A484S probably damaging Het
Usp9y A G Y: 1,316,730 (GRCm39) S1940P probably damaging Het
Zfp532 G A 18: 65,777,421 (GRCm39) V893I probably benign Het
Other mutations in Ift56
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00927:Ift56 APN 6 38,359,155 (GRCm39) splice site probably benign
IGL02049:Ift56 APN 6 38,402,067 (GRCm39) missense probably benign 0.16
IGL02403:Ift56 APN 6 38,386,373 (GRCm39) missense possibly damaging 0.95
IGL02902:Ift56 APN 6 38,402,097 (GRCm39) missense probably benign 0.21
IGL03189:Ift56 APN 6 38,402,166 (GRCm39) missense probably benign 0.00
IGL03410:Ift56 APN 6 38,362,435 (GRCm39) missense probably damaging 1.00
R0346:Ift56 UTSW 6 38,386,370 (GRCm39) missense probably damaging 1.00
R0562:Ift56 UTSW 6 38,378,064 (GRCm39) missense probably damaging 1.00
R0826:Ift56 UTSW 6 38,402,049 (GRCm39) splice site probably null
R1212:Ift56 UTSW 6 38,387,728 (GRCm39) missense probably damaging 1.00
R1778:Ift56 UTSW 6 38,386,411 (GRCm39) missense possibly damaging 0.93
R1972:Ift56 UTSW 6 38,387,738 (GRCm39) missense probably benign 0.20
R2903:Ift56 UTSW 6 38,378,037 (GRCm39) missense possibly damaging 0.61
R2904:Ift56 UTSW 6 38,378,037 (GRCm39) missense possibly damaging 0.61
R2905:Ift56 UTSW 6 38,378,037 (GRCm39) missense possibly damaging 0.61
R3788:Ift56 UTSW 6 38,380,459 (GRCm39) critical splice donor site probably null
R4222:Ift56 UTSW 6 38,372,010 (GRCm39) missense probably damaging 1.00
R4392:Ift56 UTSW 6 38,358,492 (GRCm39) start gained probably benign
R4930:Ift56 UTSW 6 38,368,475 (GRCm39) missense probably damaging 1.00
R5484:Ift56 UTSW 6 38,366,057 (GRCm39) missense probably benign 0.10
R6229:Ift56 UTSW 6 38,371,975 (GRCm39) missense probably benign 0.22
R6429:Ift56 UTSW 6 38,375,248 (GRCm39) missense possibly damaging 0.69
R6901:Ift56 UTSW 6 38,378,079 (GRCm39) missense possibly damaging 0.80
R7448:Ift56 UTSW 6 38,381,422 (GRCm39) nonsense probably null
R7554:Ift56 UTSW 6 38,362,435 (GRCm39) missense probably null 1.00
R7650:Ift56 UTSW 6 38,371,975 (GRCm39) missense probably benign 0.22
R8319:Ift56 UTSW 6 38,382,880 (GRCm39) missense probably damaging 0.98
R9270:Ift56 UTSW 6 38,366,109 (GRCm39) intron probably benign
R9417:Ift56 UTSW 6 38,386,386 (GRCm39) missense probably damaging 1.00
X0066:Ift56 UTSW 6 38,382,877 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- AACTTCTGAATGCCGCCCTC -3'
(R):5'- CACAGGGCAGCTCTTACTGAAG -3'

Sequencing Primer
(F):5'- CATTATCAACCTGGAGAGTTGGCTC -3'
(R):5'- TCTTACTGAAGAGCATAAACAACCC -3'
Posted On 2017-02-28