Incidental Mutation 'R5437:Kif3a'
ID 428435
Institutional Source Beutler Lab
Gene Symbol Kif3a
Ensembl Gene ENSMUSG00000018395
Gene Name kinesin family member 3A
Synonyms kinesin-II subunit, N-4 kinesin, Kif3, Kifl, Kns3
MMRRC Submission 043002-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5437 (G1)
Quality Score 225
Status Validated
Chromosome 11
Chromosomal Location 53458206-53492794 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 53489553 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Phenylalanine at position 135 (S135F)
Ref Sequence ENSEMBL: ENSMUSP00000116509 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000057330] [ENSMUST00000118353] [ENSMUST00000120613] [ENSMUST00000130037] [ENSMUST00000173744]
AlphaFold P28741
Predicted Effect probably benign
Transcript: ENSMUST00000057330
AA Change: S648F

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000056197
Gene: ENSMUSG00000018395
AA Change: S648F

DomainStartEndE-ValueType
KISc 12 353 9.79e-187 SMART
coiled coil region 416 593 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000118353
AA Change: S675F

PolyPhen 2 Score 0.734 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000113848
Gene: ENSMUSG00000018395
AA Change: S675F

DomainStartEndE-ValueType
KISc 12 353 9.79e-187 SMART
low complexity region 365 418 N/A INTRINSIC
coiled coil region 443 620 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000120613
AA Change: S651F

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000112782
Gene: ENSMUSG00000018395
AA Change: S651F

DomainStartEndE-ValueType
KISc 12 353 4.6e-189 SMART
coiled coil region 354 383 N/A INTRINSIC
coiled coil region 419 596 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000127858
Predicted Effect probably damaging
Transcript: ENSMUST00000130037
AA Change: S135F

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)
SMART Domains Protein: ENSMUSP00000116509
Gene: ENSMUSG00000018395
AA Change: S135F

DomainStartEndE-ValueType
SCOP:d1cm5a_ 5 88 2e-3 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000173744
AA Change: S644F

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000133432
Gene: ENSMUSG00000018395
AA Change: S644F

DomainStartEndE-ValueType
KISc 12 353 9.79e-187 SMART
low complexity region 365 406 N/A INTRINSIC
low complexity region 462 473 N/A INTRINSIC
low complexity region 481 494 N/A INTRINSIC
low complexity region 498 526 N/A INTRINSIC
Meta Mutation Damage Score 0.6449 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.1%
  • 20x: 94.7%
Validation Efficiency 97% (63/65)
MGI Phenotype PHENOTYPE: Nullizygous mutations result in embryonic lethality, failure to synthesize cilia in the embryonic node, randomization of left-right asymmetry and structural abnormalities of the neural tube, pericardium, branchial arches, and somites. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca5 G A 11: 110,210,622 (GRCm39) Q186* probably null Het
Acaca G A 11: 84,237,646 (GRCm39) probably null Het
Acsm3 C A 7: 119,377,720 (GRCm39) probably benign Het
Aoc1 C A 6: 48,884,684 (GRCm39) Q576K probably benign Het
Atp6v0a4 T A 6: 38,053,668 (GRCm39) N378I probably damaging Het
Cacna1i A T 15: 80,255,730 (GRCm39) H871L probably damaging Het
Clic4 C G 4: 134,944,557 (GRCm39) R206P probably damaging Het
Commd9 G A 2: 101,731,373 (GRCm39) G186D probably damaging Het
Cpne9 C T 6: 113,281,591 (GRCm39) probably benign Het
Crhr2 C T 6: 55,077,718 (GRCm39) V196I probably damaging Het
Dctn5 T A 7: 121,732,552 (GRCm39) probably benign Het
Dhtkd1 C T 2: 5,928,930 (GRCm39) R247Q probably benign Het
Dmrta1 G A 4: 89,579,993 (GRCm39) G318R possibly damaging Het
Dpp6 T A 5: 27,868,499 (GRCm39) Y487* probably null Het
Eef1akmt3 A T 10: 126,869,116 (GRCm39) N119K probably damaging Het
Eloa A T 4: 135,740,196 (GRCm39) L75Q probably damaging Het
Fat3 G A 9: 15,996,604 (GRCm39) T1202M probably damaging Het
Fcho2 A G 13: 98,913,982 (GRCm39) I205T possibly damaging Het
Fkbp10 A C 11: 100,311,849 (GRCm39) D174A probably damaging Het
Gcnt2 T A 13: 41,014,652 (GRCm39) F274L probably damaging Het
Gtf3c1 A T 7: 125,266,540 (GRCm39) C969S probably damaging Het
Hook3 T C 8: 26,551,450 (GRCm39) E130G probably benign Het
Itgb4 C T 11: 115,874,983 (GRCm39) R447W probably benign Het
Itsn1 T A 16: 91,615,479 (GRCm39) probably benign Het
Kif13b C T 14: 65,043,563 (GRCm39) R1788C probably damaging Het
Klf5 C T 14: 99,538,895 (GRCm39) R23* probably null Het
Lcn5 A G 2: 25,548,023 (GRCm39) I11V probably benign Het
Mpp7 A T 18: 7,458,930 (GRCm39) probably null Het
Mroh5 T C 15: 73,659,818 (GRCm39) I338V probably benign Het
Mthfd2l A G 5: 91,096,757 (GRCm39) N126S possibly damaging Het
Myo18b G T 5: 112,905,439 (GRCm39) A2053E possibly damaging Het
Naip6 A T 13: 100,439,812 (GRCm39) C318* probably null Het
Ndufs7 C T 10: 80,090,758 (GRCm39) R116C possibly damaging Het
Odr4 T G 1: 150,239,269 (GRCm39) I385L probably benign Het
Or1ad6 T C 11: 50,859,935 (GRCm39) M30T probably benign Het
Pnkd T C 1: 74,388,896 (GRCm39) V214A possibly damaging Het
Popdc2 T G 16: 38,183,263 (GRCm39) V82G probably benign Het
Prkdc A T 16: 15,587,739 (GRCm39) L2541F possibly damaging Het
Ptpn9 A T 9: 56,927,321 (GRCm39) H66L possibly damaging Het
Pygm T A 19: 6,440,412 (GRCm39) N397K probably damaging Het
Rabgap1l T A 1: 160,549,717 (GRCm39) E324D probably damaging Het
Rnf6 G A 5: 146,147,090 (GRCm39) R643C probably damaging Het
Ryr2 C T 13: 11,670,599 (GRCm39) V3466M probably damaging Het
Scn7a A G 2: 66,506,690 (GRCm39) Y1400H probably damaging Het
Septin10 T A 10: 59,012,781 (GRCm39) N279I probably damaging Het
Sh3rf2 A T 18: 42,274,079 (GRCm39) Y415F probably benign Het
Sorcs1 T C 19: 50,241,040 (GRCm39) T449A probably benign Het
Tcam1 C T 11: 106,176,249 (GRCm39) T325M probably damaging Het
Tctn1 A G 5: 122,396,942 (GRCm39) I147T probably benign Het
Tet1 G T 10: 62,650,230 (GRCm39) H30Q probably benign Het
Tmem109 A G 19: 10,849,378 (GRCm39) I159T probably damaging Het
Tmem40 C T 6: 115,735,992 (GRCm39) probably benign Het
Tnfrsf21 C T 17: 43,348,753 (GRCm39) P122S possibly damaging Het
Uaca A G 9: 60,778,733 (GRCm39) D1038G probably benign Het
Ubr2 C G 17: 47,274,623 (GRCm39) E852D probably benign Het
Ubr3 A T 2: 69,774,734 (GRCm39) N518I probably damaging Het
Unc80 T G 1: 66,693,737 (GRCm39) L2596R possibly damaging Het
Zcchc3 G A 2: 152,256,652 (GRCm39) P16S probably benign Het
Other mutations in Kif3a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01365:Kif3a APN 11 53,484,350 (GRCm39) missense possibly damaging 0.53
IGL01862:Kif3a APN 11 53,461,368 (GRCm39) missense possibly damaging 0.63
IGL02411:Kif3a APN 11 53,461,525 (GRCm39) missense probably damaging 1.00
PIT4453001:Kif3a UTSW 11 53,469,941 (GRCm39) missense probably benign 0.16
R0049:Kif3a UTSW 11 53,481,560 (GRCm39) splice site probably benign
R0049:Kif3a UTSW 11 53,481,560 (GRCm39) splice site probably benign
R0078:Kif3a UTSW 11 53,469,812 (GRCm39) missense probably benign 0.22
R0131:Kif3a UTSW 11 53,477,743 (GRCm39) missense possibly damaging 0.53
R1079:Kif3a UTSW 11 53,461,408 (GRCm39) missense possibly damaging 0.87
R1168:Kif3a UTSW 11 53,489,139 (GRCm39) missense probably damaging 1.00
R1554:Kif3a UTSW 11 53,489,154 (GRCm39) missense probably damaging 0.98
R1817:Kif3a UTSW 11 53,489,561 (GRCm39) missense probably damaging 1.00
R2022:Kif3a UTSW 11 53,461,408 (GRCm39) missense probably damaging 1.00
R2964:Kif3a UTSW 11 53,469,757 (GRCm39) missense probably damaging 1.00
R3861:Kif3a UTSW 11 53,488,805 (GRCm39) missense probably benign 0.33
R3928:Kif3a UTSW 11 53,461,441 (GRCm39) missense probably benign 0.02
R4553:Kif3a UTSW 11 53,469,745 (GRCm39) missense possibly damaging 0.93
R5158:Kif3a UTSW 11 53,479,578 (GRCm39) missense probably benign
R6621:Kif3a UTSW 11 53,469,957 (GRCm39) missense probably damaging 1.00
R7028:Kif3a UTSW 11 53,477,733 (GRCm39) nonsense probably null
R7384:Kif3a UTSW 11 53,469,681 (GRCm39) missense probably damaging 0.99
R8182:Kif3a UTSW 11 53,485,133 (GRCm39) nonsense probably null
R8493:Kif3a UTSW 11 53,489,627 (GRCm39) nonsense probably null
R8971:Kif3a UTSW 11 53,474,189 (GRCm39) missense probably damaging 1.00
R9261:Kif3a UTSW 11 53,484,248 (GRCm39) small deletion probably benign
R9577:Kif3a UTSW 11 53,475,231 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CACTGCATGACTCTGGTTTG -3'
(R):5'- TGACTGCCTTTGAGTGTAGC -3'

Sequencing Primer
(F):5'- TAGAACAGGCCTGCTCTCCAG -3'
(R):5'- GACTGCCTTTGAGTGTAGCTAAATC -3'
Posted On 2016-09-01