Mutagenetix > Incidental Mutation

Incidental Mutation 'R0490:Col6a4'

43451

Institutional Source

Beutler Lab

Gene Symbol

Col6a4

Ensembl Gene

ENSMUSG00000032572

Gene Name

collagen, type VI, alpha 4

Synonyms

Vwa6, EG235580, 1110001D15Rik, Dvwa

MMRRC Submission

038688-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0490 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

105866653-105973982 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 105890969 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Isoleucine at position 1775 (T1775I)

Ref Sequence

ENSEMBL: ENSMUSP00000112472 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000121963]

AlphaFold

A2AX52

Predicted Effect

probably damaging
Transcript: ENSMUST00000121963
AA Change: T1775I

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000112472
Gene: ENSMUSG00000032572
AA Change: T1775I

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
VWA	32	211	2.44e-35	SMART
VWA	233	410	8.67e-50	SMART
VWA	428	604	2.74e-29	SMART
VWA	632	816	4.78e-20	SMART
VWA	847	1019	3.02e-40	SMART
VWA	1028	1204	3.17e-43	SMART
VWA	1210	1391	4.73e-1	SMART
low complexity region	1444	1462	N/A	INTRINSIC
PDB:3HR2\|B	1469	1593	3e-7	PDB
low complexity region	1594	1622	N/A	INTRINSIC
low complexity region	1625	1643	N/A	INTRINSIC
low complexity region	1649	1671	N/A	INTRINSIC
Pfam:Collagen	1684	1748	1.4e-9	PFAM
VWA	1774	1953	2.18e-14	SMART
VWA	1980	2174	1.89e-9	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000213434

Predicted Effect

probably benign
Transcript: ENSMUST00000218471

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 96.2%
20x: 92.2%

Validation Efficiency

100% (60/60)

Allele List at MGI

Other mutations in this stock

Total: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
9330159F19Rik	T	A	10: 29,103,338 (GRCm39)	Y640N	probably damaging	Het
Adamts9	T	A	6: 92,849,847 (GRCm39)	Q402L	probably benign	Het
Als2cl	A	G	9: 110,724,414 (GRCm39)	T750A	probably benign	Het
Ank1	C	A	8: 23,597,890 (GRCm39)		probably benign	Het
Ap4e1	T	A	2: 126,888,106 (GRCm39)	N404K	probably damaging	Het
Atf7ip	G	T	6: 136,586,190 (GRCm39)		probably benign	Het
Bean1	A	T	8: 104,941,660 (GRCm39)	T169S	possibly damaging	Het
Bod1l	G	T	5: 41,979,235 (GRCm39)	T693N	probably damaging	Het
Ccdc81	A	T	7: 89,536,970 (GRCm39)	V226D	probably benign	Het
Cd48	A	G	1: 171,532,445 (GRCm39)	*241W	probably null	Het
Cdon	C	A	9: 35,363,978 (GRCm39)	S32Y	probably damaging	Het
Cers3	A	G	7: 66,423,438 (GRCm39)	S128G	possibly damaging	Het
Cntn6	T	C	6: 104,810,879 (GRCm39)	V641A	possibly damaging	Het
Dnah8	T	C	17: 30,919,393 (GRCm39)	V1122A	probably benign	Het
Dst	G	T	1: 34,346,449 (GRCm39)	G5102*	probably null	Het
Dvl3	C	T	16: 20,346,173 (GRCm39)		probably benign	Het
Epha5	G	T	5: 84,255,833 (GRCm39)		probably benign	Het
Fscb	G	A	12: 64,519,661 (GRCm39)	P602S	unknown	Het
Fxn	A	G	19: 24,254,543 (GRCm39)		probably null	Het
Gipc2	A	G	3: 151,808,291 (GRCm39)	L254P	possibly damaging	Het
Gm973	C	T	1: 59,597,393 (GRCm39)		probably benign	Het
Gng8	A	G	7: 16,628,908 (GRCm39)	T14A	probably benign	Het
Gsdmc3	C	T	15: 63,732,099 (GRCm39)	G309D	possibly damaging	Het
Gsr	T	A	8: 34,161,540 (GRCm39)		probably benign	Het
Gtdc1	A	T	2: 44,525,052 (GRCm39)	D152E	probably benign	Het
Herc1	A	G	9: 66,392,281 (GRCm39)	D4063G	probably damaging	Het
Hsdl2	C	T	4: 59,612,814 (GRCm39)		probably benign	Het
Iqgap3	T	C	3: 88,021,363 (GRCm39)		probably benign	Het
Kcnj10	A	G	1: 172,197,019 (GRCm39)	T178A	probably damaging	Het
Lama5	T	A	2: 179,821,962 (GRCm39)	I2958F	possibly damaging	Het
Lnx1	T	A	5: 74,781,008 (GRCm39)		probably null	Het
Lpl	A	G	8: 69,349,343 (GRCm39)	R290G	probably damaging	Het
Mamdc4	C	T	2: 25,453,593 (GRCm39)	R1196K	probably benign	Het
Mogat2	T	C	7: 98,872,351 (GRCm39)	S167G	probably benign	Het
Nek8	T	A	11: 78,058,555 (GRCm39)	I582F	probably benign	Het
Notch4	T	A	17: 34,801,864 (GRCm39)	D1237E	probably damaging	Het
Or2y8	A	G	11: 52,035,493 (GRCm39)	I288T	probably damaging	Het
Or5b104	A	G	19: 13,072,176 (GRCm39)	Y279H	probably damaging	Het
Or5b119	G	A	19: 13,456,857 (GRCm39)	A235V	probably damaging	Het
Or9i14	A	G	19: 13,792,219 (GRCm39)	L245P	probably damaging	Het
Pcdhb8	T	C	18: 37,489,833 (GRCm39)	S504P	probably damaging	Het
Pigs	T	C	11: 78,226,451 (GRCm39)	S223P	probably damaging	Het
Prkch	A	G	12: 73,806,450 (GRCm39)	I566V	probably damaging	Het
Ptpn22	T	C	3: 103,793,495 (GRCm39)	S549P	probably damaging	Het
Rita1	A	T	5: 120,749,630 (GRCm39)	F28I	probably damaging	Het
Rpgrip1l	A	T	8: 92,026,473 (GRCm39)		probably benign	Het
Slc1a1	A	G	19: 28,874,931 (GRCm39)	K170E	probably benign	Het
Spag17	C	T	3: 99,889,727 (GRCm39)	R199W	probably damaging	Het
Tas2r116	T	C	6: 132,832,984 (GRCm39)	V195A	probably benign	Het
Trav7d-3	C	A	14: 52,982,007 (GRCm39)		probably benign	Het
Trim15	T	C	17: 37,177,247 (GRCm39)	K138E	probably benign	Het
Ttn	T	A	2: 76,539,174 (GRCm39)	H34604L	probably benign	Het
Ttn	C	T	2: 76,577,876 (GRCm39)	R16012K	probably damaging	Het
Zfp948	T	C	17: 21,808,296 (GRCm39)	V496A	probably benign	Het
Zfy2	A	T	Y: 2,106,620 (GRCm39)	S671R	possibly damaging	Het
Zswim1	T	A	2: 164,667,203 (GRCm39)	Y152N	possibly damaging	Het

Other mutations in Col6a4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00573:Col6a4	APN	9	105,900,095 (GRCm39)	missense	probably benign	0.00
IGL00691:Col6a4	APN	9	105,934,606 (GRCm39)	missense	probably damaging	1.00
IGL01508:Col6a4	APN	9	105,890,804 (GRCm39)	missense	possibly damaging	0.95
IGL01580:Col6a4	APN	9	105,945,397 (GRCm39)	missense	probably damaging	1.00
IGL01610:Col6a4	APN	9	105,924,906 (GRCm39)	splice site	probably benign
IGL01813:Col6a4	APN	9	105,954,452 (GRCm39)	missense	probably damaging	1.00
IGL01933:Col6a4	APN	9	105,937,313 (GRCm39)	missense	probably benign	0.04
IGL01973:Col6a4	APN	9	105,940,093 (GRCm39)	missense	probably damaging	1.00
IGL02053:Col6a4	APN	9	105,940,294 (GRCm39)	missense	possibly damaging	0.92
IGL02063:Col6a4	APN	9	105,934,617 (GRCm39)	missense	probably benign	0.01
IGL02065:Col6a4	APN	9	105,954,302 (GRCm39)	missense	probably damaging	0.99
IGL02106:Col6a4	APN	9	105,940,304 (GRCm39)	missense	possibly damaging	0.95
IGL02220:Col6a4	APN	9	105,940,141 (GRCm39)	missense	possibly damaging	0.91
IGL02228:Col6a4	APN	9	105,945,277 (GRCm39)	missense	probably benign
IGL02234:Col6a4	APN	9	105,890,631 (GRCm39)	missense	possibly damaging	0.92
IGL02294:Col6a4	APN	9	105,943,931 (GRCm39)	missense	probably benign	0.04
IGL02314:Col6a4	APN	9	105,874,355 (GRCm39)	missense	probably damaging	0.99
IGL03065:Col6a4	APN	9	105,918,363 (GRCm39)	splice site	probably benign
IGL03086:Col6a4	APN	9	105,960,061 (GRCm39)	splice site	probably benign
IGL03185:Col6a4	APN	9	105,896,653 (GRCm39)	missense	probably damaging	0.97
R0092:Col6a4	UTSW	9	105,890,513 (GRCm39)	missense	probably benign	0.04
R0095:Col6a4	UTSW	9	105,952,555 (GRCm39)	missense	probably benign	0.03
R0230:Col6a4	UTSW	9	105,949,565 (GRCm39)	missense	probably benign	0.11
R0359:Col6a4	UTSW	9	105,874,345 (GRCm39)	missense	probably benign
R0415:Col6a4	UTSW	9	105,952,279 (GRCm39)	missense	probably damaging	0.99
R0433:Col6a4	UTSW	9	105,945,193 (GRCm39)	missense	probably damaging	0.99
R0450:Col6a4	UTSW	9	105,957,746 (GRCm39)	missense	probably damaging	1.00
R0469:Col6a4	UTSW	9	105,957,746 (GRCm39)	missense	probably damaging	1.00
R0621:Col6a4	UTSW	9	105,943,990 (GRCm39)	missense	probably damaging	0.97
R0667:Col6a4	UTSW	9	105,907,158 (GRCm39)	splice site	probably benign
R0681:Col6a4	UTSW	9	105,944,343 (GRCm39)	nonsense	probably null
R0690:Col6a4	UTSW	9	105,905,386 (GRCm39)	splice site	probably benign
R0714:Col6a4	UTSW	9	105,895,102 (GRCm39)	unclassified	probably benign
R0788:Col6a4	UTSW	9	105,949,197 (GRCm39)	missense	probably benign	0.15
R1036:Col6a4	UTSW	9	105,945,397 (GRCm39)	missense	probably damaging	1.00
R1296:Col6a4	UTSW	9	105,940,052 (GRCm39)	missense	possibly damaging	0.47
R1386:Col6a4	UTSW	9	105,940,144 (GRCm39)	missense	probably benign	0.15
R1484:Col6a4	UTSW	9	105,890,501 (GRCm39)	critical splice donor site	probably null
R1528:Col6a4	UTSW	9	105,952,419 (GRCm39)	missense	probably damaging	0.99
R1555:Col6a4	UTSW	9	105,878,085 (GRCm39)	missense	possibly damaging	0.93
R1622:Col6a4	UTSW	9	105,874,334 (GRCm39)	missense	probably benign	0.01
R1653:Col6a4	UTSW	9	105,949,608 (GRCm39)	missense	probably damaging	0.99
R1720:Col6a4	UTSW	9	105,903,671 (GRCm39)	missense	probably damaging	1.00
R1768:Col6a4	UTSW	9	105,957,299 (GRCm39)	missense	probably benign
R1941:Col6a4	UTSW	9	105,952,209 (GRCm39)	missense	probably benign	0.00
R2092:Col6a4	UTSW	9	105,937,530 (GRCm39)	missense	probably damaging	1.00
R2134:Col6a4	UTSW	9	105,943,860 (GRCm39)	missense	probably benign	0.09
R2149:Col6a4	UTSW	9	105,954,128 (GRCm39)	missense	probably benign	0.00
R2174:Col6a4	UTSW	9	105,937,331 (GRCm39)	missense	probably damaging	0.98
R2204:Col6a4	UTSW	9	105,937,331 (GRCm39)	missense	probably damaging	0.98
R2248:Col6a4	UTSW	9	105,957,158 (GRCm39)	missense	probably benign	0.15
R2568:Col6a4	UTSW	9	105,940,275 (GRCm39)	missense	possibly damaging	0.90
R3750:Col6a4	UTSW	9	105,897,864 (GRCm39)	critical splice acceptor site	probably null
R3751:Col6a4	UTSW	9	105,949,313 (GRCm39)	missense	probably damaging	0.98
R3776:Col6a4	UTSW	9	105,928,900 (GRCm39)	nonsense	probably null
R3872:Col6a4	UTSW	9	105,890,858 (GRCm39)	missense	possibly damaging	0.95
R4043:Col6a4	UTSW	9	105,949,610 (GRCm39)	nonsense	probably null
R4056:Col6a4	UTSW	9	105,903,665 (GRCm39)	missense	probably damaging	0.98
R4212:Col6a4	UTSW	9	105,952,569 (GRCm39)	missense	probably benign	0.28
R4417:Col6a4	UTSW	9	105,949,215 (GRCm39)	missense	probably damaging	0.99
R4683:Col6a4	UTSW	9	105,957,329 (GRCm39)	missense	probably benign	0.00
R4719:Col6a4	UTSW	9	105,945,451 (GRCm39)	missense	probably damaging	0.99
R4791:Col6a4	UTSW	9	105,957,401 (GRCm39)	missense	possibly damaging	0.68
R4833:Col6a4	UTSW	9	105,949,178 (GRCm39)	missense	probably benign	0.00
R4886:Col6a4	UTSW	9	105,937,271 (GRCm39)	missense	probably benign	0.00
R4998:Col6a4	UTSW	9	105,867,977 (GRCm39)	utr 3 prime	probably benign
R5091:Col6a4	UTSW	9	105,952,262 (GRCm39)	missense	probably damaging	1.00
R5113:Col6a4	UTSW	9	105,944,159 (GRCm39)	missense	possibly damaging	0.89
R5129:Col6a4	UTSW	9	105,890,576 (GRCm39)	missense	probably damaging	0.98
R5231:Col6a4	UTSW	9	105,902,730 (GRCm39)	missense	probably damaging	0.96
R5297:Col6a4	UTSW	9	105,952,066 (GRCm39)	missense	probably benign	0.02
R5352:Col6a4	UTSW	9	105,938,743 (GRCm39)	missense	probably damaging	1.00
R5438:Col6a4	UTSW	9	105,890,895 (GRCm39)	missense	possibly damaging	0.95
R5518:Col6a4	UTSW	9	105,949,387 (GRCm39)	missense	possibly damaging	0.68
R5657:Col6a4	UTSW	9	105,949,397 (GRCm39)	missense	probably damaging	0.99
R5660:Col6a4	UTSW	9	105,873,315 (GRCm39)	missense	probably benign	0.01
R5662:Col6a4	UTSW	9	105,945,200 (GRCm39)	missense	probably damaging	0.99
R5777:Col6a4	UTSW	9	105,890,895 (GRCm39)	missense	possibly damaging	0.95
R5800:Col6a4	UTSW	9	105,957,474 (GRCm39)	missense	probably damaging	0.99
R5929:Col6a4	UTSW	9	105,940,243 (GRCm39)	missense	probably benign	0.15
R5999:Col6a4	UTSW	9	105,945,120 (GRCm39)	missense	probably benign	0.11
R6243:Col6a4	UTSW	9	105,890,589 (GRCm39)	missense	possibly damaging	0.95
R6285:Col6a4	UTSW	9	105,952,185 (GRCm39)	missense	probably damaging	0.96
R6288:Col6a4	UTSW	9	105,945,462 (GRCm39)	missense	probably damaging	0.99
R6361:Col6a4	UTSW	9	105,943,902 (GRCm39)	missense	probably benign	0.28
R6485:Col6a4	UTSW	9	105,954,069 (GRCm39)	critical splice donor site	probably null
R6490:Col6a4	UTSW	9	105,952,191 (GRCm39)	nonsense	probably null
R6537:Col6a4	UTSW	9	105,945,153 (GRCm39)	missense	possibly damaging	0.87
R6598:Col6a4	UTSW	9	105,877,611 (GRCm39)	missense	probably damaging	0.99
R6643:Col6a4	UTSW	9	105,877,830 (GRCm39)	missense	probably damaging	0.96
R6905:Col6a4	UTSW	9	105,937,517 (GRCm39)	splice site	probably null
R6944:Col6a4	UTSW	9	105,949,370 (GRCm39)	missense	probably damaging	0.98
R7015:Col6a4	UTSW	9	105,910,954 (GRCm39)	critical splice donor site	probably null
R7027:Col6a4	UTSW	9	105,944,213 (GRCm39)	missense	probably damaging	1.00
R7088:Col6a4	UTSW	9	105,877,885 (GRCm39)	missense	possibly damaging	0.56
R7200:Col6a4	UTSW	9	105,949,448 (GRCm39)	missense	possibly damaging	0.68
R7238:Col6a4	UTSW	9	105,877,519 (GRCm39)	missense	probably damaging	0.99
R7273:Col6a4	UTSW	9	105,877,656 (GRCm39)	missense	possibly damaging	0.92
R7335:Col6a4	UTSW	9	105,954,091 (GRCm39)	missense	possibly damaging	0.90
R7418:Col6a4	UTSW	9	105,900,114 (GRCm39)	missense	probably damaging	1.00
R7421:Col6a4	UTSW	9	105,897,994 (GRCm39)	missense	probably damaging	0.99
R7530:Col6a4	UTSW	9	105,945,589 (GRCm39)	missense	probably damaging	0.99
R7600:Col6a4	UTSW	9	105,944,198 (GRCm39)	missense	possibly damaging	0.86
R7701:Col6a4	UTSW	9	105,960,087 (GRCm39)	missense	probably benign	0.17
R7830:Col6a4	UTSW	9	105,952,589 (GRCm39)	missense	probably damaging	0.99
R7881:Col6a4	UTSW	9	105,957,497 (GRCm39)	missense	probably benign	0.14
R8157:Col6a4	UTSW	9	105,945,097 (GRCm39)	missense	possibly damaging	0.92
R8292:Col6a4	UTSW	9	105,954,076 (GRCm39)	missense	probably benign	0.01
R8309:Col6a4	UTSW	9	105,952,414 (GRCm39)	missense	probably benign	0.08
R8336:Col6a4	UTSW	9	105,952,528 (GRCm39)	missense	possibly damaging	0.65
R8359:Col6a4	UTSW	9	105,945,583 (GRCm39)	missense	probably benign	0.00
R8530:Col6a4	UTSW	9	105,957,704 (GRCm39)	missense	probably benign	0.31
R8556:Col6a4	UTSW	9	105,944,252 (GRCm39)	missense	probably damaging	0.96
R8832:Col6a4	UTSW	9	105,949,353 (GRCm39)	missense	probably benign
R9001:Col6a4	UTSW	9	105,944,370 (GRCm39)	missense	probably benign	0.26
R9009:Col6a4	UTSW	9	105,954,404 (GRCm39)	missense	probably benign	0.38
R9069:Col6a4	UTSW	9	105,952,138 (GRCm39)	missense	possibly damaging	0.85
R9155:Col6a4	UTSW	9	105,952,209 (GRCm39)	missense	probably benign
R9175:Col6a4	UTSW	9	105,957,560 (GRCm39)	missense	probably benign
R9176:Col6a4	UTSW	9	105,938,755 (GRCm39)	missense	probably damaging	1.00
R9295:Col6a4	UTSW	9	105,957,734 (GRCm39)	missense	probably damaging	1.00
R9298:Col6a4	UTSW	9	105,945,534 (GRCm39)	missense	probably damaging	0.96
R9389:Col6a4	UTSW	9	105,877,983 (GRCm39)	missense	probably damaging	1.00
R9424:Col6a4	UTSW	9	105,945,271 (GRCm39)	missense	probably benign	0.30
R9576:Col6a4	UTSW	9	105,945,271 (GRCm39)	missense	probably benign	0.30
RF022:Col6a4	UTSW	9	105,954,207 (GRCm39)	missense	probably damaging	0.99
X0025:Col6a4	UTSW	9	105,877,654 (GRCm39)	missense	probably damaging	0.99
Z1176:Col6a4	UTSW	9	105,878,069 (GRCm39)	missense	probably damaging	0.99
Z1176:Col6a4	UTSW	9	105,877,996 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AACCTCATAGTGGCCCCAAGGTTC -3'
(R):5'- GACAGGCACAAACCGTGTCTTTTC -3'

Sequencing Primer
(F):5'- TTCCCCGATGGTCTGACAAG -3'
(R):5'- ACAAACCGTGTCTTTTCCCTTC -3'

Posted On

2013-05-23