Mutagenetix > Incidental Mutation

Incidental Mutation 'R7060:Col2a1'

548218

Institutional Source

Beutler Lab

Gene Symbol

Col2a1

Ensembl Gene

ENSMUSG00000022483

Gene Name

collagen, type II, alpha 1

Synonyms

Rgsc413, M100413, Rgsc856, Col2a-1, M100856, Del1, Col2a, Col2, Lpk

MMRRC Submission

045157-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R7060 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

97873483-97902525 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 97874022 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Lysine at position 1387 (Q1387K)

Ref Sequence

ENSEMBL: ENSMUSP00000085693 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023123] [ENSMUST00000088355]

AlphaFold

P28481

Predicted Effect

unknown
Transcript: ENSMUST00000023123
AA Change: Q1455K

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: Q1455K

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
VWC	34	88	1.59e-21	SMART
Pfam:Collagen	115	175	1.3e-11	PFAM
Pfam:Collagen	199	260	7.2e-11	PFAM
Pfam:Collagen	258	317	1.3e-12	PFAM
Pfam:Collagen	312	377	4e-9	PFAM
low complexity region	395	411	N/A	INTRINSIC
low complexity region	416	451	N/A	INTRINSIC
internal_repeat_5	456	468	5.45e-5	PROSPERO
low complexity region	471	513	N/A	INTRINSIC
internal_repeat_3	516	619	3.99e-13	PROSPERO
internal_repeat_1	524	567	1.6e-17	PROSPERO
low complexity region	621	633	N/A	INTRINSIC
low complexity region	636	655	N/A	INTRINSIC
low complexity region	659	687	N/A	INTRINSIC
low complexity region	696	753	N/A	INTRINSIC
internal_repeat_5	756	768	5.45e-5	PROSPERO
low complexity region	783	804	N/A	INTRINSIC
Pfam:Collagen	852	918	1.1e-8	PFAM
Pfam:Collagen	876	941	1.9e-9	PFAM
Pfam:Collagen	900	966	2.4e-9	PFAM
Pfam:Collagen	983	1049	2.1e-10	PFAM
low complexity region	1062	1081	N/A	INTRINSIC
Pfam:Collagen	1101	1172	3.4e-9	PFAM
Pfam:Collagen	1158	1218	1.3e-9	PFAM
COLFI	1252	1487	3.06e-184	SMART

Predicted Effect

unknown
Transcript: ENSMUST00000088355
AA Change: Q1387K

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: Q1387K

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
Pfam:Collagen	47	107	1.2e-11	PFAM
Pfam:Collagen	131	192	7.2e-11	PFAM
Pfam:Collagen	190	249	1.3e-12	PFAM
low complexity region	262	314	N/A	INTRINSIC
Pfam:Collagen	327	405	3.5e-7	PFAM
Pfam:Collagen	361	429	7.6e-10	PFAM
internal_repeat_3	448	551	1.3e-13	PROSPERO
internal_repeat_7	454	466	2.86e-5	PROSPERO
internal_repeat_1	456	499	4.05e-18	PROSPERO
internal_repeat_6	481	504	1.7e-5	PROSPERO
low complexity region	553	565	N/A	INTRINSIC
low complexity region	568	587	N/A	INTRINSIC
low complexity region	591	619	N/A	INTRINSIC
low complexity region	628	685	N/A	INTRINSIC
internal_repeat_4	688	712	8.3e-12	PROSPERO
low complexity region	715	736	N/A	INTRINSIC
low complexity region	747	784	N/A	INTRINSIC
Pfam:Collagen	808	878	9.8e-9	PFAM
Pfam:Collagen	832	898	2.1e-9	PFAM
Pfam:Collagen	916	979	7.2e-10	PFAM
Pfam:Collagen	937	1005	2.1e-8	PFAM
Pfam:Collagen	973	1049	6e-7	PFAM
Pfam:Collagen	1030	1094	1.5e-10	PFAM
Pfam:Collagen	1088	1150	1.4e-9	PFAM
COLFI	1184	1419	3.06e-184	SMART

Meta Mutation Damage Score

0.0893

Coding Region Coverage

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

Validation Efficiency

96% (78/81)

MGI Phenotype

FUNCTION: This gene encodes the alpha-1 subunit of the fibril-forming type II collagen, the major component of cartilage and the vitreous humor of the eye. The encoded preproprotein forms homotrimeric, triple helical procollagen that undergoes proteolytic processing during fibirl formation. Mice harboring certain mutations in this gene exhibit severe chondrodysplasia characterized by short limbs and trunch, craniofacial deformities and cleft palate. A complete lack of the encoded protein in mice results in postnatal lethality. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mutations in this locus affect cartilage development. Homozygotes die perinatally with anomalies such as shortened limbs without epiphiseal growth plates, cleft palate and persistence of notochord. Heterozygotes are dwarfed with reduced cartilage matrix. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcg4	T	A	9: 44,186,425 (GRCm39)	T535S	probably benign	Het
Adamts19	A	T	18: 58,970,712 (GRCm39)	R99*	probably null	Het
Alg6	C	T	4: 99,650,198 (GRCm39)	L473F	possibly damaging	Het
Ankar	A	T	1: 72,695,272 (GRCm39)	N893K	probably benign	Het
Ankrd54	G	A	15: 78,939,739 (GRCm39)	A183V	possibly damaging	Het
Anpep	G	T	7: 79,491,542 (GRCm39)	T153K	probably benign	Het
Arap1	A	G	7: 101,058,564 (GRCm39)		probably null	Het
Aspg	A	T	12: 112,089,387 (GRCm39)	T392S	probably benign	Het
B230307C23Rik	A	C	16: 97,811,331 (GRCm39)	R68S	probably benign	Het
Bdp1	G	C	13: 100,196,002 (GRCm39)	N1253K	probably damaging	Het
Ccrl2	G	A	9: 110,884,682 (GRCm39)	S272F	probably damaging	Het
Cdon	T	C	9: 35,398,205 (GRCm39)	L974P	probably damaging	Het
Celsr1	C	A	15: 85,916,856 (GRCm39)	E372D	probably benign	Het
Cers1	A	T	8: 70,768,555 (GRCm39)	M16L	possibly damaging	Het
Ddx39b	G	A	17: 35,471,726 (GRCm39)	V291M	probably damaging	Het
Dppa2	T	A	16: 48,136,076 (GRCm39)	S143T	probably benign	Het
Dpy19l1	A	T	9: 24,334,419 (GRCm39)	M583K	possibly damaging	Het
Eno3	A	T	11: 70,552,245 (GRCm39)	D299V	possibly damaging	Het
Epha8	C	T	4: 136,658,469 (GRCm39)	V969M	probably damaging	Het
Fcgbp	A	T	7: 27,791,358 (GRCm39)	H873L	probably benign	Het
Fhad1	CGG	CG	4: 141,645,602 (GRCm39)		probably null	Het
Fntb	A	C	12: 76,934,649 (GRCm39)	N173T	possibly damaging	Het
Gins2	T	A	8: 121,308,880 (GRCm39)	M125L	probably benign	Het
Gys1	G	A	7: 45,089,437 (GRCm39)	A199T	probably damaging	Het
Herpud1	C	A	8: 95,117,391 (GRCm39)	H116N	probably benign	Het
Hoga1	C	A	19: 42,048,685 (GRCm39)	Y134*	probably null	Het
Il10ra	A	G	9: 45,167,522 (GRCm39)	I343T	probably benign	Het
Inava	T	C	1: 136,147,935 (GRCm39)	K339R	possibly damaging	Het
Inpp5j	C	T	11: 3,450,133 (GRCm39)		probably null	Het
Itpkb	T	C	1: 180,160,695 (GRCm39)	S274P	probably damaging	Het
Kalrn	C	T	16: 34,177,418 (GRCm39)	C249Y	probably damaging	Het
Klhl35	G	C	7: 99,117,665 (GRCm39)	A70P	possibly damaging	Het
Lhx1	A	G	11: 84,411,108 (GRCm39)		probably null	Het
Lmbrd1	T	C	1: 24,732,047 (GRCm39)	V88A	probably benign	Het
Macc1	T	G	12: 119,411,190 (GRCm39)	L653V	probably damaging	Het
Madd	T	C	2: 91,007,452 (GRCm39)	D220G	probably damaging	Het
Mllt10	T	A	2: 18,164,371 (GRCm39)	H300Q	possibly damaging	Het
Mlxipl	G	A	5: 135,161,169 (GRCm39)	A363T	possibly damaging	Het
Mus81	G	T	19: 5,537,821 (GRCm39)	D78E	probably benign	Het
Mxd1	A	T	6: 86,630,141 (GRCm39)	L26M	probably damaging	Het
Nhsl1	C	T	10: 18,402,251 (GRCm39)	T1159M	probably damaging	Het
Nos1ap	A	G	1: 170,165,694 (GRCm39)	S190P	possibly damaging	Het
Nwd1	A	C	8: 73,393,322 (GRCm39)	D195A	probably damaging	Het
Or12d13	G	T	17: 37,647,352 (GRCm39)	T257N	probably benign	Het
Or6k4	A	T	1: 173,964,376 (GRCm39)	D22V	probably benign	Het
Or8c14-ps1	G	A	9: 38,101,392 (GRCm39)	V124I	probably damaging	Het
Or8k24	T	A	2: 86,216,569 (GRCm39)	R64S	possibly damaging	Het
Otof	T	C	5: 30,545,700 (GRCm39)	D500G	possibly damaging	Het
Pcgf5	T	A	19: 36,420,339 (GRCm39)	Y190*	probably null	Het
Pdcd11	C	T	19: 47,099,418 (GRCm39)	T839I	probably benign	Het
Ppard	G	C	17: 28,517,886 (GRCm39)	S318T	probably benign	Het
Ppfia2	A	G	10: 106,597,970 (GRCm39)	K178E	probably damaging	Het
Ppm1n	G	T	7: 19,013,187 (GRCm39)	R255S	probably damaging	Het
Ppp1r21	A	G	17: 88,887,972 (GRCm39)	Y693C	probably damaging	Het
Ppp2r5d	A	T	17: 46,998,279 (GRCm39)	V169E	possibly damaging	Het
Prc1	A	T	7: 79,954,121 (GRCm39)	T53S	probably benign	Het
Pwp2	A	C	10: 78,009,084 (GRCm39)		probably null	Het
Rab5c	G	A	11: 100,610,789 (GRCm39)	R40C	probably damaging	Het
Ring1	A	G	17: 34,242,364 (GRCm39)	C48R	probably damaging	Het
Rpap1	T	C	2: 119,604,043 (GRCm39)	D496G	probably damaging	Het
Rspo4	C	A	2: 151,714,998 (GRCm39)	Q212K	unknown	Het
Samd9l	T	A	6: 3,372,716 (GRCm39)	D1515V	probably damaging	Het
Serinc3	T	C	2: 163,478,879 (GRCm39)	T83A	probably benign	Het
Setd5	A	C	6: 113,094,343 (GRCm39)	D420A	probably damaging	Het
Sidt2	T	C	9: 45,864,544 (GRCm39)	T62A	possibly damaging	Het
Smarcal1	T	C	1: 72,652,101 (GRCm39)	V621A	probably damaging	Het
Srcin1	A	G	11: 97,464,711 (GRCm39)	L12P	probably damaging	Het
Stx18	G	A	5: 38,278,599 (GRCm39)	D165N	possibly damaging	Het
Sumf2	A	G	5: 129,883,341 (GRCm39)	K139E	possibly damaging	Het
Tdo2	A	T	3: 81,876,866 (GRCm39)	I102N	probably damaging	Het
Tdp1	T	A	12: 99,877,947 (GRCm39)	S410T	probably benign	Het
Tmem94	A	T	11: 115,683,764 (GRCm39)	I726F	probably damaging	Het
Ttc21a	A	G	9: 119,795,742 (GRCm39)	E1192G	probably damaging	Het
Ttc8	T	C	12: 98,909,726 (GRCm39)	I52T	probably benign	Het
Vmn2r99	A	T	17: 19,614,826 (GRCm39)	R849*	probably null	Het
Wwc1	T	C	11: 35,806,003 (GRCm39)	K77E	possibly damaging	Het
Xirp2	A	T	2: 67,345,952 (GRCm39)	E2731V	probably damaging	Het
Zfp1006	A	C	8: 129,945,613 (GRCm39)	I404R	probably benign	Het
Zfp423	G	A	8: 88,509,507 (GRCm39)	T258I	probably damaging	Het

Other mutations in Col2a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01025:Col2a1	APN	15	97,874,054 (GRCm39)	missense	unknown
IGL01286:Col2a1	APN	15	97,892,759 (GRCm39)	missense	unknown
IGL01369:Col2a1	APN	15	97,875,707 (GRCm39)	missense	unknown
IGL01747:Col2a1	APN	15	97,889,273 (GRCm39)	splice site	probably benign
IGL02086:Col2a1	APN	15	97,884,618 (GRCm39)	splice site	probably null
IGL02549:Col2a1	APN	15	97,875,680 (GRCm39)	missense	unknown
IGL03289:Col2a1	APN	15	97,878,762 (GRCm39)	missense	unknown
IGL03369:Col2a1	APN	15	97,879,923 (GRCm39)	missense	unknown
Foreseen	UTSW	15	97,874,674 (GRCm39)	missense	unknown
FR4304:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
FR4340:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
FR4342:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
FR4589:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
LCD18:Col2a1	UTSW	15	97,886,862 (GRCm39)	splice site	probably null
R0124:Col2a1	UTSW	15	97,896,743 (GRCm39)	missense	unknown
R0227:Col2a1	UTSW	15	97,874,636 (GRCm39)	missense	unknown
R0690:Col2a1	UTSW	15	97,878,073 (GRCm39)	missense	unknown
R1434:Col2a1	UTSW	15	97,877,532 (GRCm39)	missense	probably damaging	0.96
R1473:Col2a1	UTSW	15	97,880,789 (GRCm39)	splice site	probably benign
R1577:Col2a1	UTSW	15	97,877,083 (GRCm39)	missense	probably damaging	1.00
R1598:Col2a1	UTSW	15	97,877,131 (GRCm39)	missense	probably damaging	0.99
R1837:Col2a1	UTSW	15	97,894,522 (GRCm39)	splice site	probably benign
R2153:Col2a1	UTSW	15	97,885,461 (GRCm39)	missense	unknown
R2965:Col2a1	UTSW	15	97,873,976 (GRCm39)	missense	unknown
R2966:Col2a1	UTSW	15	97,873,976 (GRCm39)	missense	unknown
R3710:Col2a1	UTSW	15	97,888,788 (GRCm39)	splice site	probably benign
R3838:Col2a1	UTSW	15	97,898,462 (GRCm39)	intron	probably benign
R3838:Col2a1	UTSW	15	97,886,857 (GRCm39)	missense	unknown
R4112:Col2a1	UTSW	15	97,881,582 (GRCm39)	missense	probably benign	0.18
R4417:Col2a1	UTSW	15	97,896,466 (GRCm39)	missense	unknown
R4656:Col2a1	UTSW	15	97,874,057 (GRCm39)	missense	unknown
R4960:Col2a1	UTSW	15	97,874,030 (GRCm39)	missense	unknown
R5008:Col2a1	UTSW	15	97,877,550 (GRCm39)	missense	probably benign	0.28
R5435:Col2a1	UTSW	15	97,898,391 (GRCm39)	intron	probably benign
R5473:Col2a1	UTSW	15	97,885,370 (GRCm39)	missense	unknown
R6042:Col2a1	UTSW	15	97,898,451 (GRCm39)	intron	probably benign
R6118:Col2a1	UTSW	15	97,896,448 (GRCm39)	missense	unknown
R6183:Col2a1	UTSW	15	97,886,671 (GRCm39)	missense	unknown
R6187:Col2a1	UTSW	15	97,886,671 (GRCm39)	missense	unknown
R6401:Col2a1	UTSW	15	97,883,773 (GRCm39)	missense	unknown
R6550:Col2a1	UTSW	15	97,874,674 (GRCm39)	missense	unknown
R6568:Col2a1	UTSW	15	97,875,157 (GRCm39)	missense	unknown
R6988:Col2a1	UTSW	15	97,902,335 (GRCm39)	missense	unknown
R7069:Col2a1	UTSW	15	97,896,469 (GRCm39)	missense	unknown
R7167:Col2a1	UTSW	15	97,898,337 (GRCm39)	missense	unknown
R7294:Col2a1	UTSW	15	97,885,168 (GRCm39)	splice site	probably null
R7392:Col2a1	UTSW	15	97,878,032 (GRCm39)	nonsense	probably null
R7491:Col2a1	UTSW	15	97,874,040 (GRCm39)	missense	not run
R7583:Col2a1	UTSW	15	97,874,065 (GRCm39)	missense	unknown
R7665:Col2a1	UTSW	15	97,874,581 (GRCm39)	missense	unknown
R7872:Col2a1	UTSW	15	97,898,458 (GRCm39)	nonsense	probably null
R8177:Col2a1	UTSW	15	97,874,654 (GRCm39)	missense	unknown
R8306:Col2a1	UTSW	15	97,888,849 (GRCm39)	critical splice acceptor site	probably null
R9343:Col2a1	UTSW	15	97,877,775 (GRCm39)	missense	probably damaging	0.99
R9458:Col2a1	UTSW	15	97,876,242 (GRCm39)	missense	unknown
Z1177:Col2a1	UTSW	15	97,896,226 (GRCm39)	missense	unknown
Z1177:Col2a1	UTSW	15	97,881,854 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGCCATTCAGTGCAGATCC -3'
(R):5'- ACAAGTAGAGGAGGGCTCTACC -3'

Sequencing Primer
(F):5'- CATTCAGTGCAGATCCTGGAG -3'
(R):5'- GCTCTACCATCAAGGGGACAATTG -3'

Posted On

2019-05-13