Mutagenetix > Incidental Mutation

Incidental Mutation 'R5660:Col6a4'

444041

Institutional Source

Beutler Lab

Gene Symbol

Col6a4

Ensembl Gene

ENSMUSG00000032572

Gene Name

collagen, type VI, alpha 4

Synonyms

Vwa6, EG235580, 1110001D15Rik, Dvwa

MMRRC Submission

043173-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5660 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

105866653-105973982 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 105873315 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 2227 (S2227P)

Ref Sequence

ENSEMBL: ENSMUSP00000112472 (fasta)

Gene Model

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

AlphaFold

A2AX52

Predicted Effect

probably benign
Transcript: ENSMUST00000121963
AA Change: S2227P

PolyPhen 2 Score 0.010 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000112472
Gene: ENSMUSG00000032572
AA Change: S2227P

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: ENSMUST00000149207

Predicted Effect

probably benign
Transcript: ENSMUST00000218471

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.4%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 46 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc8	T	C	7: 45,757,828 (GRCm39)	N1307S	probably benign	Het
Abcf1	A	T	17: 36,274,539 (GRCm39)	D41E	possibly damaging	Het
Adamts13	T	C	2: 26,886,761 (GRCm39)	V966A	probably benign	Het
Adamts2	A	T	11: 50,667,472 (GRCm39)	D470V	probably damaging	Het
Adar	T	C	3: 89,642,901 (GRCm39)	F261L	probably damaging	Het
Akap3	C	T	6: 126,842,254 (GRCm39)	A291V	probably damaging	Het
Akr1c6	G	A	13: 4,499,053 (GRCm39)	V214I	probably benign	Het
Ano5	G	A	7: 51,233,562 (GRCm39)	R658H	possibly damaging	Het
Arhgap11a	T	A	2: 113,672,255 (GRCm39)	I238F	possibly damaging	Het
Atg2b	A	T	12: 105,615,383 (GRCm39)	Y1024*	probably null	Het
Cad	T	A	5: 31,234,191 (GRCm39)	D1956E	probably damaging	Het
Cbs	A	T	17: 31,843,220 (GRCm39)	I237N	probably damaging	Het
Ccdc81	T	C	7: 89,542,337 (GRCm39)	T180A	probably benign	Het
Cftr	T	A	6: 18,313,686 (GRCm39)	N1303K	probably benign	Het
Crebbp	A	T	16: 3,972,722 (GRCm39)	M324K	possibly damaging	Het
Dst	A	G	1: 34,321,574 (GRCm39)	K4363R	probably damaging	Het
Eif2b4	A	T	5: 31,348,500 (GRCm39)	Y238N	probably benign	Het
Fam83c	G	A	2: 155,671,509 (GRCm39)	A642V	probably benign	Het
Fat2	T	A	11: 55,175,002 (GRCm39)	T1904S	probably benign	Het
Flt3	T	C	5: 147,306,291 (GRCm39)	N279S	possibly damaging	Het
Galnt4	A	G	10: 98,945,397 (GRCm39)	N374S	probably benign	Het
Gm14401	T	A	2: 176,778,224 (GRCm39)	H103Q	probably damaging	Het
Gm5422	A	T	10: 31,126,048 (GRCm39)		noncoding transcript	Het
Helb	G	A	10: 119,946,984 (GRCm39)	Q110*	probably null	Het
Ido1	T	C	8: 25,081,558 (GRCm39)	D41G	probably damaging	Het
Igfn1	A	G	1: 135,898,152 (GRCm39)	S805P	probably benign	Het
Matr3	C	A	18: 35,705,147 (GRCm39)	A24E	probably damaging	Het
Mmp23	C	T	4: 155,735,710 (GRCm39)	C287Y	probably damaging	Het
Mrnip	A	G	11: 50,087,918 (GRCm39)	R147G	probably null	Het
Msh6	A	G	17: 88,292,147 (GRCm39)	K301E	possibly damaging	Het
Or12d13	A	G	17: 37,647,535 (GRCm39)	L196P	probably damaging	Het
Or8g4	G	A	9: 39,662,063 (GRCm39)	C127Y	probably damaging	Het
Ptar1	T	A	19: 23,671,776 (GRCm39)	C60S	probably benign	Het
Rora	A	G	9: 68,561,203 (GRCm39)	S11G	probably benign	Het
Rps6ka5	G	T	12: 100,585,839 (GRCm39)	H151Q	possibly damaging	Het
Sgsh	A	G	11: 119,241,807 (GRCm39)	S100P	probably damaging	Het
Simc1	A	G	13: 54,694,902 (GRCm39)	T1229A	probably benign	Het
Slc26a11	T	C	11: 119,248,804 (GRCm39)	Y62H	probably damaging	Het
Slc5a8	C	T	10: 88,755,290 (GRCm39)	L466F	possibly damaging	Het
Smg1	C	T	7: 117,742,570 (GRCm39)	V3215I	probably benign	Het
Smyd2	G	A	1: 189,617,579 (GRCm39)	P285L	possibly damaging	Het
Themis2	T	C	4: 132,523,567 (GRCm39)		probably null	Het
Tln1	A	G	4: 43,547,732 (GRCm39)	V743A	probably damaging	Het
Tpo	T	A	12: 30,150,495 (GRCm39)	N462Y	possibly damaging	Het
Wnt2	T	A	6: 18,028,145 (GRCm39)	M30L	probably benign	Het
Zfyve9	T	C	4: 108,576,365 (GRCm39)	I239V	probably benign	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
R0490:Col6a4	UTSW	9	105,890,969 (GRCm39)	missense	probably damaging	0.99
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
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'- AAATGTCTTCCTTTTGCTGGCG -3'
(R):5'- ATGATGCTAAGCACCCGATG -3'

Sequencing Primer
(F):5'- GGCGTTTCCTGATCAATGTC -3'
(R):5'- TGGTATGAATCCTCAGCCCAGAG -3'

Posted On

2016-11-09