Mutagenetix > Incidental Mutation

Incidental Mutation 'R7657:Itga6'

591242

Institutional Source

Beutler Lab

Gene Symbol

Itga6

Ensembl Gene

ENSMUSG00000027111

Gene Name

integrin alpha 6

Synonyms

5033401O05Rik, Cd49f

MMRRC Submission

045733-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7657 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

71617236-71688761 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 71676595 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 993 (A993T)

Ref Sequence

ENSEMBL: ENSMUSP00000028522 (fasta)

Gene Model

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

AlphaFold

Q61739

Predicted Effect

probably benign
Transcript: ENSMUST00000028522
AA Change: A993T

PolyPhen 2 Score 0.403 (Sensitivity: 0.89; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000028522
Gene: ENSMUSG00000027111
AA Change: A993T

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

possibly damaging
Transcript: ENSMUST00000112101
AA Change: A993T

PolyPhen 2 Score 0.876 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000107729
Gene: ENSMUSG00000027111
AA Change: A993T

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

SMART Domains

Protein: ENSMUSP00000118086
Gene: ENSMUSG00000027111
AA Change: A586T

Domain	Start	End	E-Value	Type
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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

100% (80/80)

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2310033P09Rik	A	G	11: 59,099,337 (GRCm39)	E28G	possibly damaging	Het
Acot6	G	A	12: 84,153,304 (GRCm39)	G182D	possibly damaging	Het
Actl9	A	G	17: 33,652,014 (GRCm39)	T25A	probably benign	Het
Adam26b	G	A	8: 43,974,579 (GRCm39)	T141I	possibly damaging	Het
Agl	T	C	3: 116,572,812 (GRCm39)	H148R		Het
Angptl1	A	G	1: 156,684,790 (GRCm39)	I320V	probably benign	Het
Arhgef10	C	T	8: 15,029,893 (GRCm39)	R932C	probably damaging	Het
Atp13a2	A	G	4: 140,719,815 (GRCm39)	E91G	possibly damaging	Het
Bptf	T	A	11: 106,965,555 (GRCm39)	E1213V	probably damaging	Het
C530025M09Rik	A	G	2: 149,672,541 (GRCm39)	V198A	unknown	Het
Casd1	A	T	6: 4,619,773 (GRCm39)	I173F	probably benign	Het
Ccng2	C	G	5: 93,421,202 (GRCm39)	S237R	probably benign	Het
Col1a2	A	T	6: 4,527,152 (GRCm39)	K627M	probably null	Het
Ctcfl	G	A	2: 172,955,449 (GRCm39)	T271I	possibly damaging	Het
Dctn2	T	C	10: 127,102,383 (GRCm39)	Y6H	probably damaging	Het
Denr	T	C	5: 124,046,263 (GRCm39)	V31A	probably damaging	Het
Entpd7	T	C	19: 43,713,906 (GRCm39)	F422L	possibly damaging	Het
Fastkd5	G	C	2: 130,458,176 (GRCm39)	P138R	probably benign	Het
Fmn1	G	T	2: 113,355,538 (GRCm39)	A758S	unknown	Het
Fmo2	A	G	1: 162,716,413 (GRCm39)	V58A	probably damaging	Het
Fmo6	A	G	1: 162,750,285 (GRCm39)	I257T	probably benign	Het
Foxn1	T	C	11: 78,256,790 (GRCm39)	T302A	probably benign	Het
Ganab	C	T	19: 8,884,721 (GRCm39)	L175F	probably damaging	Het
Gga1	A	T	15: 78,773,327 (GRCm39)		probably null	Het
Gjd3	G	T	11: 98,873,586 (GRCm39)	S86*	probably null	Het
Gm1330	A	G	2: 148,841,154 (GRCm39)		probably null	Het
Gm18596	A	C	10: 77,577,947 (GRCm39)	S176A	unknown	Het
Gnl2	A	G	4: 124,923,951 (GRCm39)	S10G	probably benign	Het
Gpsm2	G	A	3: 108,608,061 (GRCm39)	A239V	probably damaging	Het
Grik2	T	C	10: 49,659,247 (GRCm39)	R37G	probably benign	Het
Grm3	A	G	5: 9,561,452 (GRCm39)		probably null	Het
Gtpbp3	T	C	8: 71,943,765 (GRCm39)	L216P	probably benign	Het
Hhla1	T	C	15: 65,837,308 (GRCm39)	T99A	probably damaging	Het
Igtp	A	T	11: 58,097,654 (GRCm39)	Q275L	probably benign	Het
Jakmip3	T	A	7: 138,620,903 (GRCm39)	I234N	probably damaging	Het
Kcnh7	A	G	2: 62,566,379 (GRCm39)	F851L	probably damaging	Het
Krr1	A	G	10: 111,811,504 (GRCm39)	Y66C	probably damaging	Het
Krt33a	T	A	11: 99,906,693 (GRCm39)	Q94L	probably benign	Het
Mat1a	A	T	14: 40,844,476 (GRCm39)	K369*	probably null	Het
Mbd1	T	G	18: 74,407,804 (GRCm39)	L277R	probably damaging	Het
Mmp21	C	T	7: 133,280,562 (GRCm39)	G136D	probably benign	Het
Mroh3	A	G	1: 136,109,532 (GRCm39)	Y892H	possibly damaging	Het
Ncbp3	G	A	11: 72,964,193 (GRCm39)	R381Q	probably damaging	Het
Nlrp2	T	A	7: 5,322,167 (GRCm39)	I827L	probably benign	Het
Nrip1	T	A	16: 76,091,587 (GRCm39)		probably null	Het
Or2ak4	A	T	11: 58,648,755 (GRCm39)	D88V	probably benign	Het
Or4f6	A	G	2: 111,839,093 (GRCm39)	V146A	probably benign	Het
Or5w13	C	T	2: 87,523,336 (GRCm39)	V297I	probably damaging	Het
Oxt	C	T	2: 130,418,710 (GRCm39)	P107L	possibly damaging	Het
Pcdhga2	G	A	18: 37,803,481 (GRCm39)	V442M	probably damaging	Het
Phtf1	T	G	3: 103,876,429 (GRCm39)	S10A	probably benign	Het
Plb1	A	C	5: 32,487,211 (GRCm39)	N902T	probably damaging	Het
Plppr3	T	C	10: 79,702,272 (GRCm39)	I267V	probably benign	Het
Pms2	C	A	5: 143,856,357 (GRCm39)	H278Q	possibly damaging	Het
Pmvk	T	A	3: 89,376,158 (GRCm39)	S154T	possibly damaging	Het
Polr3b	T	A	10: 84,491,855 (GRCm39)	M338K	probably damaging	Het
Ppp1r21	T	A	17: 88,863,110 (GRCm39)	I283N	probably damaging	Het
Ptprj	A	T	2: 90,282,501 (GRCm39)		probably null	Het
Rft1	T	A	14: 30,388,724 (GRCm39)	L216H	probably damaging	Het
Rpl3	G	A	15: 79,965,258 (GRCm39)	P174S	probably benign	Het
Rtl1	T	C	12: 109,561,818 (GRCm39)	D7G	possibly damaging	Het
Slc13a2	A	G	11: 78,289,223 (GRCm39)	V496A	probably damaging	Het
Slc14a1	A	G	18: 78,156,879 (GRCm39)		probably null	Het
Slc8a3	T	C	12: 81,361,158 (GRCm39)	R554G	probably damaging	Het
Spata31d1b	T	C	13: 59,863,577 (GRCm39)	S242P	possibly damaging	Het
Spocd1	G	A	4: 129,823,535 (GRCm39)	V111I		Het
Stxbp5l	G	A	16: 37,030,534 (GRCm39)	A479V	probably null	Het
Tasor2	A	G	13: 3,623,777 (GRCm39)	S2058P	probably damaging	Het
Tmem238	C	G	7: 4,792,226 (GRCm39)	G106R	probably damaging	Het
Trak1	T	G	9: 121,301,652 (GRCm39)	Y803D	probably damaging	Het
Trim5	T	C	7: 103,925,884 (GRCm39)	S226G	possibly damaging	Het
Trim6	T	A	7: 103,881,068 (GRCm39)	D282E	possibly damaging	Het
Ube2e2	A	G	14: 18,586,997 (GRCm38)	V121A	probably benign	Het
Ufd1	T	G	16: 18,636,713 (GRCm39)	M77R	probably benign	Het
Unc13c	C	T	9: 73,441,185 (GRCm39)		probably null	Het
Wfs1	A	G	5: 37,125,578 (GRCm39)	S438P	probably benign	Het
Zbtb6	A	C	2: 37,319,087 (GRCm39)	D280E	probably benign	Het
Zfp595	G	A	13: 67,465,817 (GRCm39)	L152F	probably damaging	Het
Zfpm2	A	G	15: 40,966,671 (GRCm39)	E1052G	possibly damaging	Het
Zmym5	A	G	14: 57,041,653 (GRCm39)	V150A	probably benign	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
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
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
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'- AACAGCACATTTCTAGAGGTGC -3'
(R):5'- ACACCTGCATTACTAGGCTTGG -3'

Sequencing Primer
(F):5'- CACATTTCTAGAGGTGCGGCTC -3'
(R):5'- CATTACTAGGCTTGGCTCGG -3'

Posted On

2019-11-12