Mutagenetix > Incidental Mutation

Incidental Mutation 'R1713:Itga6'

190735

Institutional Source

Beutler Lab

Gene Symbol

Itga6

Ensembl Gene

ENSMUSG00000027111

Gene Name

integrin alpha 6

Synonyms

5033401O05Rik, Cd49f

MMRRC Submission

039746-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1713 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

71617236-71688761 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 71617546 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 22 (T22A)

Ref Sequence

ENSEMBL: ENSMUSP00000107729 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000028522] [ENSMUST00000112101]

AlphaFold

Q61739

Predicted Effect

probably benign
Transcript: ENSMUST00000028522
AA Change: T22A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000028522
Gene: ENSMUSG00000027111
AA Change: T22A

Domain	Start	End	E-Value	Type
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: T22A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000107729
Gene: ENSMUSG00000027111
AA Change: T22A

Domain	Start	End	E-Value	Type
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

noncoding transcript
Transcript: ENSMUST00000133124

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152009

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

98% (96/98)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921539E11Rik	T	A	4: 103,127,964 (GRCm39)	I54F	possibly damaging	Het
Ackr1	A	T	1: 173,159,916 (GRCm39)	H134Q	probably benign	Het
Agtr1b	A	T	3: 20,370,473 (GRCm39)	F44L	probably benign	Het
Ahnak	G	A	19: 8,989,173 (GRCm39)	D3486N	possibly damaging	Het
Akap9	T	C	5: 4,089,345 (GRCm39)		probably null	Het
Anks6	T	A	4: 47,039,726 (GRCm39)	Q495L	probably benign	Het
Arpp21	A	G	9: 111,896,237 (GRCm39)	S684P	probably damaging	Het
Ash1l	A	G	3: 88,983,531 (GRCm39)	E2911G	probably damaging	Het
Avpi1	C	T	19: 42,113,248 (GRCm39)	E70K	probably damaging	Het
Btbd17	G	T	11: 114,686,650 (GRCm39)	P9T	probably benign	Het
C4b	A	G	17: 34,948,245 (GRCm39)		probably benign	Het
Carm1	T	C	9: 21,497,785 (GRCm39)	V385A	probably damaging	Het
Casd1	A	G	6: 4,624,104 (GRCm39)	D299G	probably damaging	Het
Clca3a1	T	A	3: 144,730,307 (GRCm39)	K179N	probably benign	Het
Col1a2	T	C	6: 4,538,691 (GRCm39)	S1204P	unknown	Het
Col24a1	C	T	3: 145,072,624 (GRCm39)	Q780*	probably null	Het
Cxadr	C	A	16: 78,131,133 (GRCm39)	N216K	probably damaging	Het
Daam1	C	T	12: 71,942,656 (GRCm39)	T40I	unknown	Het
Dab2	C	T	15: 6,459,182 (GRCm39)	P365S	possibly damaging	Het
Dnah1	A	T	14: 31,001,139 (GRCm39)	I2402N	probably damaging	Het
Dscaml1	T	A	9: 45,663,988 (GRCm39)	S1954R	possibly damaging	Het
Dync2h1	T	C	9: 7,131,891 (GRCm39)	T1639A	probably benign	Het
Ebf1	A	T	11: 44,815,393 (GRCm39)	I336F	probably damaging	Het
Ebna1bp2	A	G	4: 118,482,881 (GRCm39)	N290S	possibly damaging	Het
Gabra2	A	G	5: 71,171,906 (GRCm39)	I110T	probably benign	Het
Galk2	A	G	2: 125,773,210 (GRCm39)	N203S	probably benign	Het
Gria4	T	C	9: 4,424,448 (GRCm39)	T806A	probably benign	Het
Impg2	A	G	16: 56,080,889 (GRCm39)	T789A	probably benign	Het
Itgb4	T	A	11: 115,894,315 (GRCm39)	I1312N	probably damaging	Het
Kdm4c	A	G	4: 74,216,721 (GRCm39)	D160G	probably benign	Het
Kdr	A	G	5: 76,129,127 (GRCm39)	V173A	probably benign	Het
Kif14	T	C	1: 136,455,202 (GRCm39)	S1575P	probably benign	Het
Lcp1	G	A	14: 75,436,884 (GRCm39)		probably null	Het
Lipe	C	A	7: 25,084,750 (GRCm39)	S516I	probably damaging	Het
Lrrc61	G	A	6: 48,545,708 (GRCm39)	R177Q	possibly damaging	Het
Macf1	A	G	4: 123,272,487 (GRCm39)	I6429T	probably damaging	Het
Map3k4	C	T	17: 12,468,458 (GRCm39)	E1012K	probably benign	Het
Map3k5	T	C	10: 19,986,593 (GRCm39)	F936L	possibly damaging	Het
Mllt3	A	T	4: 87,701,901 (GRCm39)	N497K	probably damaging	Het
Moxd1	G	A	10: 24,157,394 (GRCm39)	G342D	probably damaging	Het
Mtdh	A	C	15: 34,114,985 (GRCm39)	Q202H	possibly damaging	Het
Nav1	A	G	1: 135,522,972 (GRCm39)		probably benign	Het
Nop56	T	C	2: 130,119,886 (GRCm39)	V109A	possibly damaging	Het
Obscn	T	C	11: 58,970,712 (GRCm39)	D2540G	probably damaging	Het
Omg	T	C	11: 79,393,679 (GRCm39)	I60V	probably benign	Het
Or10q12	A	T	19: 13,746,659 (GRCm39)	T318S	probably benign	Het
Or12e9	A	T	2: 87,202,290 (GRCm39)	Y138F	probably damaging	Het
Osbpl5	G	A	7: 143,248,110 (GRCm39)	H652Y	probably damaging	Het
Parvb	T	C	15: 84,182,192 (GRCm39)		probably benign	Het
Pcdhb3	A	C	18: 37,436,375 (GRCm39)	E780D	probably benign	Het
Pik3c3	A	G	18: 30,456,639 (GRCm39)	D723G	possibly damaging	Het
Prkdc	T	C	16: 15,612,958 (GRCm39)	V3172A	probably benign	Het
Psme4	G	T	11: 30,756,310 (GRCm39)	W272L	probably damaging	Het
Rem1	G	A	2: 152,476,455 (GRCm39)	V238M	probably damaging	Het
Rhobtb1	A	C	10: 69,108,601 (GRCm39)	S434R	probably benign	Het
Rhobtb1	G	C	10: 69,108,602 (GRCm39)	S434T	possibly damaging	Het
Rnf8	T	C	17: 29,853,735 (GRCm39)	F413S	probably damaging	Het
Rpn2	A	G	2: 157,156,888 (GRCm39)	N497S	probably damaging	Het
Rsbn1l	G	T	5: 21,156,488 (GRCm39)	P99Q	probably benign	Het
Serpinb3b	A	T	1: 107,083,164 (GRCm39)	M246K	probably benign	Het
Sgsm2	T	C	11: 74,787,652 (GRCm39)	E19G	probably null	Het
Shank1	A	G	7: 43,969,161 (GRCm39)	H352R	unknown	Het
Slc17a7	A	G	7: 44,819,728 (GRCm39)	I177V	probably benign	Het
Slc28a2	T	A	2: 122,281,494 (GRCm39)	F228I	probably damaging	Het
Slc35b4	C	T	6: 34,147,484 (GRCm39)	V35I	probably benign	Het
Slc38a1	T	C	15: 96,476,641 (GRCm39)	I407V	probably damaging	Het
Slc39a13	A	G	2: 90,893,442 (GRCm39)	V326A	probably damaging	Het
Slc44a5	T	C	3: 153,944,743 (GRCm39)	L120P	probably damaging	Het
Slfn3	T	C	11: 83,104,140 (GRCm39)	I214T	probably damaging	Het
Slitrk3	A	C	3: 72,957,024 (GRCm39)	S583A	probably benign	Het
Snx14	T	C	9: 88,297,728 (GRCm39)	Y180C	probably damaging	Het
Sorl1	T	A	9: 41,907,538 (GRCm39)	K1483I	probably benign	Het
Ssrp1	C	A	2: 84,871,104 (GRCm39)	H247N	probably damaging	Het
Stk39	A	T	2: 68,137,460 (GRCm39)		probably benign	Het
Syde1	C	T	10: 78,421,530 (GRCm39)	G674R	probably damaging	Het
Tent4a	A	T	13: 69,651,170 (GRCm39)	I565N	probably benign	Het
Themis3	G	A	17: 66,862,848 (GRCm39)	S370L	probably benign	Het
Tll1	T	A	8: 64,554,907 (GRCm39)	N259Y	probably damaging	Het
Tnip2	T	G	5: 34,661,175 (GRCm39)		probably benign	Het
Top2b	T	C	14: 16,409,823 (GRCm38)	V830A	probably benign	Het
Trpm8	T	A	1: 88,292,802 (GRCm39)	N934K	probably damaging	Het
Ttc14	A	G	3: 33,857,069 (GRCm39)	Y179C	probably damaging	Het
Ttn	T	G	2: 76,573,965 (GRCm39)	I17316L	possibly damaging	Het
Tufm	T	C	7: 126,086,871 (GRCm39)	V52A	probably benign	Het
Vamp8	T	A	6: 72,365,270 (GRCm39)	N20I	probably benign	Het
Vmn1r170	A	T	7: 23,306,288 (GRCm39)	H230L	probably benign	Het
Vmn2r50	T	G	7: 9,771,731 (GRCm39)	T657P	probably damaging	Het
Xirp2	G	A	2: 67,342,762 (GRCm39)	G1668R	probably benign	Het
Zik1	C	A	7: 10,224,311 (GRCm39)	R262L	possibly damaging	Het
Zscan25	T	G	5: 145,220,501 (GRCm39)	Y99D	probably damaging	Het

Other mutations in Itga6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
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
R5386:Itga6	UTSW	2	71,671,494 (GRCm39)	missense	probably damaging	1.00
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'- GGAGTCCCGGTCACTCGATAAAAC -3'
(R):5'- AAGTCTTGGGCCGAAGAAGTGC -3'

Sequencing Primer
(F):5'- GGTCACTCGATAAAACGCTTG -3'
(R):5'- agggcagggcaaggtag -3'

Posted On

2014-05-14