Incidental Mutation 'R5386:Itga6'
ID 500969
Institutional Source Beutler Lab
Gene Symbol Itga6
Ensembl Gene ENSMUSG00000027111
Gene Name integrin alpha 6
Synonyms 5033401O05Rik, Cd49f
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5386 (G1)
Quality Score 225
Status Not validated
Chromosome 2
Chromosomal Location 71617236-71688761 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 71671494 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Arginine at position 341 (S341R)
Gene Model predicted gene model for transcript(s): [ENSMUST00000028522] [ENSMUST00000112101]
AlphaFold Q61739
Predicted Effect probably benign
Transcript: ENSMUST00000028522
AA Change: S748R

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000028522
Gene: ENSMUSG00000027111
AA Change: S748R

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Int_alpha 40 101 3.12e-6 SMART
Int_alpha 254 303 2.7e-1 SMART
Int_alpha 312 368 1.46e-11 SMART
Int_alpha 373 426 9.73e-17 SMART
Int_alpha 428 483 5.83e0 SMART
SCOP:d1m1xa2 629 786 5e-32 SMART
SCOP:d1m1xa3 797 1017 3e-55 SMART
Pfam:Integrin_alpha 1038 1052 3.2e-7 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000112101
AA Change: S748R

PolyPhen 2 Score 0.007 (Sensitivity: 0.96; Specificity: 0.75)
SMART Domains Protein: ENSMUSP00000107729
Gene: ENSMUSG00000027111
AA Change: S748R

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Int_alpha 40 101 3.12e-6 SMART
Int_alpha 254 303 2.7e-1 SMART
Int_alpha 312 368 1.46e-11 SMART
Int_alpha 373 426 9.73e-17 SMART
Int_alpha 428 483 5.83e0 SMART
SCOP:d1m1xa2 629 786 4e-32 SMART
SCOP:d1m1xa3 797 1017 4e-55 SMART
low complexity region 1058 1070 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000155249
AA Change: S341R

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000118086
Gene: ENSMUSG00000027111
AA Change: S341R

DomainStartEndE-ValueType
Pfam:Integrin_alpha2 58 533 4.7e-131 PFAM
transmembrane domain 609 631 N/A INTRINSIC
Pfam:Integrin_alpha 632 646 6.2e-8 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000155596
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a protein that is a member of the integrin superfamily. Integrins are transmembrane receptors involved cell adhesion and signaling, and they are subdivided based on the heterodimer formation of alpha and beta chains. This protein has been shown to heterodimerize with beta 4 to bind laminin and to form the main component of hemidesmosomes, which mediate attachment of epithelia to basement membranes. In mouse, deficiency of this gene is associated with absence of hemidesmosomes, severe skin blistering, and early post-natal death. In humans mutations of this gene are associated with epidermolysis bullosa. Alternative splicing results in multiple transcript variants that encode different protein isoforms. [provided by RefSeq, May 2013]
PHENOTYPE: Homozygotes for a targeted null mutation exhibit severe blistering of the skin and other epithelia, absence of hemidesmosomes, altered laminin deposition in brain, and ectopic neuroblastic outgrowths on the brain and in the eye. Mutants die at birth. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 134 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcc12 T G 8: 87,244,118 (GRCm39) K1012Q possibly damaging Het
Afmid G A 11: 117,718,968 (GRCm39) G33R probably benign Het
Agbl3 G T 6: 34,776,131 (GRCm39) W207C probably damaging Het
Ajuba T C 14: 54,807,855 (GRCm39) Y459C probably damaging Het
Ak2 T C 4: 128,901,965 (GRCm39) S213P probably benign Het
Alk T A 17: 72,182,007 (GRCm39) N1339Y probably damaging Het
Angpt1 T C 15: 42,301,761 (GRCm39) S416G probably damaging Het
Ank2 C T 3: 126,775,582 (GRCm39) V854M probably benign Het
Ankrd61 G T 5: 143,828,482 (GRCm39) N122K possibly damaging Het
Armc9 T A 1: 86,126,011 (GRCm39) L34Q probably null Het
Aspg T A 12: 112,089,466 (GRCm39) V418E probably benign Het
Baz1b C T 5: 135,266,913 (GRCm39) R1241C probably damaging Het
Bclaf1 T C 10: 20,201,338 (GRCm39) V201A possibly damaging Het
C1ql3 A T 2: 13,009,169 (GRCm39) D225E probably damaging Het
Capn9 A G 8: 125,332,279 (GRCm39) T417A possibly damaging Het
Card14 C T 11: 119,208,115 (GRCm39) R62C probably damaging Het
Cc2d2a A G 5: 43,887,383 (GRCm39) N1271S probably benign Het
Ccpg1 G A 9: 72,920,326 (GRCm39) S647N probably benign Het
Cdv3 T C 9: 103,232,429 (GRCm39) K133R possibly damaging Het
Cep128 A C 12: 90,966,345 (GRCm39) S1087R probably benign Het
Cep70 T A 9: 99,163,128 (GRCm39) L325Q probably damaging Het
Chit1 T G 1: 134,077,192 (GRCm39) F332V probably damaging Het
Chodl C A 16: 78,743,585 (GRCm39) T219K probably damaging Het
Cntn4 T C 6: 106,158,765 (GRCm39) L10P possibly damaging Het
Copg1 G T 6: 87,867,189 (GRCm39) M87I possibly damaging Het
Cplane1 G A 15: 8,223,897 (GRCm39) G887R probably damaging Het
Cyp3a59 A G 5: 146,022,578 (GRCm39) Y28C probably benign Het
Dchs1 A C 7: 105,407,236 (GRCm39) V2119G probably damaging Het
Dedd T C 1: 171,165,951 (GRCm39) L23P probably damaging Het
Dmxl2 A G 9: 54,286,041 (GRCm39) S2715P probably benign Het
Dnah9 T C 11: 65,920,182 (GRCm39) N2237S probably damaging Het
Drosha A G 15: 12,842,207 (GRCm39) I337V probably benign Het
Duox2 A G 2: 122,125,617 (GRCm39) V330A probably benign Het
Dusp11 T C 6: 85,924,587 (GRCm39) *322W probably null Het
Dusp8 T A 7: 141,643,730 (GRCm39) Q61L possibly damaging Het
Ears2 G C 7: 121,643,600 (GRCm39) T426S probably benign Het
Elmo1 T C 13: 20,784,380 (GRCm39) Y646H probably benign Het
Eps15 T A 4: 109,178,422 (GRCm39) I220K possibly damaging Het
Faap100 T A 11: 120,268,458 (GRCm39) E105V possibly damaging Het
Fam171a2 C A 11: 102,328,693 (GRCm39) V689L possibly damaging Het
Fam91a1 G A 15: 58,320,243 (GRCm39) S645N probably benign Het
Fancg G A 4: 43,007,076 (GRCm39) Q234* probably null Het
Garre1 A G 7: 33,941,813 (GRCm39) F120L probably damaging Het
Gid4 T A 11: 60,323,268 (GRCm39) probably null Het
Gm7361 A C 5: 26,463,903 (GRCm39) T53P probably benign Het
Golgb1 T A 16: 36,732,677 (GRCm39) C641* probably null Het
Gon4l T A 3: 88,765,803 (GRCm39) M409K probably benign Het
Gpatch8 A T 11: 102,399,053 (GRCm39) probably null Het
Gpr156 T A 16: 37,768,671 (GRCm39) V64E possibly damaging Het
Grid2 T A 6: 63,908,089 (GRCm39) I243K probably damaging Het
Gucy2g G A 19: 55,203,548 (GRCm39) A750V probably damaging Het
Hdac5 T C 11: 102,092,967 (GRCm39) E590G possibly damaging Het
Herc3 T A 6: 58,851,263 (GRCm39) M504K probably damaging Het
Hif1a A G 12: 73,990,867 (GRCm39) E713G probably benign Het
Hmx3 A G 7: 131,146,033 (GRCm39) D247G probably damaging Het
Hoxd11 G T 2: 74,513,163 (GRCm39) E143* probably null Het
Ifitm3 T C 7: 140,590,554 (GRCm39) N2S probably benign Het
Il17f T C 1: 20,848,181 (GRCm39) Q99R probably benign Het
Itgam A G 7: 127,707,152 (GRCm39) N661S probably benign Het
Jag1 A T 2: 136,937,464 (GRCm39) H303Q possibly damaging Het
Kcnh8 T A 17: 53,033,023 (GRCm39) N103K probably benign Het
Kdm6b T C 11: 69,291,636 (GRCm39) probably benign Het
Keg1 A C 19: 12,691,902 (GRCm39) N63T probably damaging Het
Klf12 T A 14: 100,137,595 (GRCm39) H317L probably damaging Het
Lrp1 A T 10: 127,427,983 (GRCm39) V530E probably damaging Het
Mrgpra6 A G 7: 46,838,629 (GRCm39) C190R probably damaging Het
Myo1a G T 10: 127,541,766 (GRCm39) E102* probably null Het
Napa A T 7: 15,850,397 (GRCm39) E265D probably benign Het
Ncam1 A C 9: 49,476,174 (GRCm39) V305G probably damaging Het
Nek8 T C 11: 78,061,263 (GRCm39) probably null Het
Or10ag53 C T 2: 87,082,827 (GRCm39) P182L probably benign Het
Or11g24 T A 14: 50,662,846 (GRCm39) V290E possibly damaging Het
Or4a70 G T 2: 89,324,481 (GRCm39) Y58* probably null Het
Or4f52 T C 2: 111,061,539 (GRCm39) T200A probably benign Het
Or52a20 T C 7: 103,366,562 (GRCm39) F254L probably benign Het
Or5ak4 T C 2: 85,161,979 (GRCm39) T88A probably benign Het
Or5h23 T A 16: 58,906,253 (GRCm39) M198L probably benign Het
Or8c11 A T 9: 38,289,281 (GRCm39) I29F probably benign Het
Or8g2b A G 9: 39,751,126 (GRCm39) Y132C possibly damaging Het
Pabpc4 A G 4: 123,188,790 (GRCm39) Q417R probably benign Het
Panx3 A T 9: 37,580,320 (GRCm39) M11K probably damaging Het
Pcbp1 C T 6: 86,502,471 (GRCm39) E143K probably damaging Het
Pdcd7 G A 9: 65,265,974 (GRCm39) W477* probably null Het
Pi4k2a G A 19: 42,078,954 (GRCm39) S5N probably damaging Het
Plag1 T A 4: 3,904,075 (GRCm39) Q372L probably benign Het
Plce1 C A 19: 38,748,535 (GRCm39) N1755K probably damaging Het
Pld4 G T 12: 112,730,422 (GRCm39) E102* probably null Het
Pnlip A G 19: 58,668,039 (GRCm39) N345S probably benign Het
Ppm1e A T 11: 87,249,377 (GRCm39) L118Q possibly damaging Het
Prkra T G 2: 76,469,622 (GRCm39) T146P probably damaging Het
Prpf8 A G 11: 75,386,625 (GRCm39) D1038G probably damaging Het
Prss51 T A 14: 64,334,543 (GRCm39) V108E probably damaging Het
Prxl2b T A 4: 154,983,462 (GRCm39) M1L probably benign Het
Ptch1 A G 13: 63,692,857 (GRCm39) Y181H probably damaging Het
Reln A G 5: 22,244,527 (GRCm39) V817A probably benign Het
Rictor C A 15: 6,818,985 (GRCm39) Q1403K probably benign Het
Rims1 T A 1: 22,482,469 (GRCm39) I882F probably damaging Het
Rnf19a A G 15: 36,242,185 (GRCm39) V618A probably benign Het
Ryr1 A T 7: 28,816,841 (GRCm39) I65N probably damaging Het
S1pr2 T C 9: 20,878,890 (GRCm39) T313A probably benign Het
Serpine2 A T 1: 79,799,004 (GRCm39) Y83* probably null Het
Sfi1 A ATCTTCCCAAAGCCAGTGC 11: 3,103,384 (GRCm39) probably benign Het
Sgip1 T C 4: 102,772,256 (GRCm39) V215A probably benign Het
Sgsm3 T C 15: 80,892,200 (GRCm39) V256A probably benign Het
Shroom4 T A X: 6,497,523 (GRCm39) C894* probably null Het
Slc14a2 T A 18: 78,229,055 (GRCm39) D306V possibly damaging Het
Slc28a2b C A 2: 122,353,259 (GRCm39) L480I probably benign Het
Slc4a10 A T 2: 62,120,402 (GRCm39) E843V probably damaging Het
Smyd4 T A 11: 75,280,982 (GRCm39) C152S probably damaging Het
Snx10 T C 6: 51,552,952 (GRCm39) Y32H probably damaging Het
Sorl1 T C 9: 41,968,580 (GRCm39) T558A possibly damaging Het
Spata31d1b G A 13: 59,866,866 (GRCm39) C1338Y possibly damaging Het
Sppl2c T A 11: 104,078,127 (GRCm39) I309K possibly damaging Het
Stard9 A G 2: 120,531,111 (GRCm39) E2456G probably damaging Het
Stx1b A T 7: 127,414,575 (GRCm39) D16E probably benign Het
Tecpr2 T C 12: 110,881,887 (GRCm39) V152A probably damaging Het
Tedc1 T C 12: 113,120,302 (GRCm39) V47A probably benign Het
Tep1 A T 14: 51,105,774 (GRCm39) L82Q probably damaging Het
Tgm4 A G 9: 122,885,559 (GRCm39) Y367C probably damaging Het
Tle1 C T 4: 72,060,081 (GRCm39) V258M probably damaging Het
Tm9sf1 C T 14: 55,880,301 (GRCm39) G32D possibly damaging Het
Tmco2 A G 4: 120,963,181 (GRCm39) L106P probably damaging Het
Tmem131 A T 1: 36,911,639 (GRCm39) C103S possibly damaging Het
Tmprss7 T A 16: 45,489,891 (GRCm39) I444F possibly damaging Het
Trank1 T C 9: 111,191,470 (GRCm39) V493A probably benign Het
Trim80 A T 11: 115,338,843 (GRCm39) T558S probably benign Het
Trmt6 C A 2: 132,650,703 (GRCm39) A302S probably benign Het
Ttc17 A T 2: 94,133,985 (GRCm39) W1067R probably damaging Het
Tulp4 T A 17: 6,286,568 (GRCm39) V1532D probably damaging Het
Ubqlnl T G 7: 103,798,424 (GRCm39) I358L probably benign Het
Ulk3 T A 9: 57,498,023 (GRCm39) I108N possibly damaging Het
Vps13b A T 15: 35,640,674 (GRCm39) probably null Het
Vwa3a A G 7: 120,389,365 (GRCm39) K68E possibly damaging Het
Zfp746 G T 6: 48,041,110 (GRCm39) H538N possibly damaging Het
Other mutations in Itga6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00832:Itga6 APN 2 71,668,606 (GRCm39) splice site probably null
IGL00902:Itga6 APN 2 71,679,738 (GRCm39) missense probably benign 0.39
IGL01360:Itga6 APN 2 71,617,670 (GRCm39) splice site probably null
IGL01621:Itga6 APN 2 71,656,000 (GRCm39) missense probably benign 0.02
IGL01877:Itga6 APN 2 71,668,624 (GRCm39) missense probably benign
IGL02332:Itga6 APN 2 71,668,717 (GRCm39) missense possibly damaging 0.63
IGL02556:Itga6 APN 2 71,669,027 (GRCm39) missense probably benign 0.20
IGL02713:Itga6 APN 2 71,647,057 (GRCm39) missense possibly damaging 0.79
IGL02811:Itga6 APN 2 71,657,076 (GRCm39) missense probably damaging 0.98
IGL03171:Itga6 APN 2 71,671,673 (GRCm39) critical splice donor site probably null
isle_royale UTSW 2 71,617,577 (GRCm39) missense probably benign 0.04
PIT4418001:Itga6 UTSW 2 71,664,414 (GRCm39) missense probably benign 0.06
R0070:Itga6 UTSW 2 71,657,060 (GRCm39) unclassified probably benign
R0611:Itga6 UTSW 2 71,650,404 (GRCm39) missense possibly damaging 0.84
R1404:Itga6 UTSW 2 71,669,060 (GRCm39) missense probably benign
R1404:Itga6 UTSW 2 71,669,060 (GRCm39) missense probably benign
R1439:Itga6 UTSW 2 71,664,378 (GRCm39) missense probably damaging 1.00
R1487:Itga6 UTSW 2 71,673,584 (GRCm39) missense possibly damaging 0.87
R1713:Itga6 UTSW 2 71,617,546 (GRCm39) missense probably benign
R1720:Itga6 UTSW 2 71,650,510 (GRCm39) missense probably damaging 1.00
R1816:Itga6 UTSW 2 71,671,153 (GRCm39) missense probably benign 0.00
R1866:Itga6 UTSW 2 71,664,414 (GRCm39) missense probably benign
R2009:Itga6 UTSW 2 71,647,025 (GRCm39) missense probably benign 0.26
R2018:Itga6 UTSW 2 71,648,828 (GRCm39) missense probably benign 0.16
R2171:Itga6 UTSW 2 71,650,358 (GRCm39) missense probably damaging 1.00
R2189:Itga6 UTSW 2 71,655,961 (GRCm39) missense probably benign 0.00
R2289:Itga6 UTSW 2 71,648,873 (GRCm39) missense probably damaging 0.99
R2399:Itga6 UTSW 2 71,650,358 (GRCm39) missense probably damaging 1.00
R4437:Itga6 UTSW 2 71,655,982 (GRCm39) missense probably benign 0.42
R4482:Itga6 UTSW 2 71,686,259 (GRCm39) missense probably damaging 1.00
R4773:Itga6 UTSW 2 71,652,788 (GRCm39) missense probably benign 0.13
R4786:Itga6 UTSW 2 71,669,034 (GRCm39) missense possibly damaging 0.80
R4898:Itga6 UTSW 2 71,668,717 (GRCm39) missense possibly damaging 0.77
R5074:Itga6 UTSW 2 71,656,779 (GRCm39) missense probably benign
R5591:Itga6 UTSW 2 71,670,934 (GRCm39) missense probably damaging 1.00
R6024:Itga6 UTSW 2 71,617,577 (GRCm39) missense probably benign 0.04
R6174:Itga6 UTSW 2 71,664,053 (GRCm39) missense possibly damaging 0.88
R6210:Itga6 UTSW 2 71,664,351 (GRCm39) critical splice acceptor site probably null
R6432:Itga6 UTSW 2 71,664,116 (GRCm39) missense possibly damaging 0.75
R6644:Itga6 UTSW 2 71,671,468 (GRCm39) missense probably damaging 1.00
R7354:Itga6 UTSW 2 71,650,574 (GRCm39) missense probably damaging 1.00
R7402:Itga6 UTSW 2 71,683,897 (GRCm39) missense probably benign 0.05
R7479:Itga6 UTSW 2 71,668,680 (GRCm39) nonsense probably null
R7635:Itga6 UTSW 2 71,673,577 (GRCm39) missense probably benign 0.00
R7657:Itga6 UTSW 2 71,676,595 (GRCm39) missense probably benign 0.40
R7737:Itga6 UTSW 2 71,652,787 (GRCm39) missense probably benign 0.38
R7782:Itga6 UTSW 2 71,671,879 (GRCm39) missense probably damaging 0.98
R8062:Itga6 UTSW 2 71,672,087 (GRCm39) missense probably benign 0.11
R8312:Itga6 UTSW 2 71,686,297 (GRCm39) missense probably benign
R8698:Itga6 UTSW 2 71,673,618 (GRCm39) missense probably benign
R9080:Itga6 UTSW 2 71,673,633 (GRCm39) missense probably benign
R9169:Itga6 UTSW 2 71,647,015 (GRCm39) missense possibly damaging 0.74
R9209:Itga6 UTSW 2 71,671,477 (GRCm39) missense probably benign 0.27
R9267:Itga6 UTSW 2 71,668,756 (GRCm39) missense probably benign 0.00
R9483:Itga6 UTSW 2 71,679,834 (GRCm39) missense probably benign 0.03
R9747:Itga6 UTSW 2 71,656,871 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TTACAGAGAACTGAGGGCTTTCC -3'
(R):5'- GGAGAGGTTGAAGTTACGCTTAC -3'

Sequencing Primer
(F):5'- CCCTGTAAGTGTTTTTGAGAAAGCAG -3'
(R):5'- ACGTTTCCAACTTCAGATTAATATCC -3'
Posted On 2017-12-01