Mutagenetix > Incidental Mutation

Incidental Mutation 'R6187:Col2a1'

502271

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

044327-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6187 (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 97886671 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Asparagine at position 378 (T378N)

Ref Sequence

ENSEMBL: ENSMUSP00000085693 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000023123] [ENSMUST00000088355] [ENSMUST00000131560]

AlphaFold

P28481

Predicted Effect

unknown
Transcript: ENSMUST00000023123
AA Change: T446N

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: T446N

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: T378N

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: T378N

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000128547

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131560

SMART Domains

Protein: ENSMUSP00000116951
Gene: ENSMUSG00000022483

Domain	Start	End	E-Value	Type
signal peptide	1	25	N/A	INTRINSIC
VWC	34	88	1.59e-21	SMART
low complexity region	109	132	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000131910

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

99% (79/80)

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: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	T	A	11: 9,259,085 (GRCm39)	L2937H	probably damaging	Het
Abca3	A	G	17: 24,627,141 (GRCm39)	I1281V	possibly damaging	Het
Adam2	A	T	14: 66,306,068 (GRCm39)	S138T	possibly damaging	Het
Adamts4	C	T	1: 171,078,562 (GRCm39)	P61S	probably damaging	Het
Adamts6	C	T	13: 104,433,933 (GRCm39)	P121S	probably damaging	Het
Afg3l2	G	T	18: 67,554,329 (GRCm39)	L458M	probably damaging	Het
Ak1	G	A	2: 32,523,489 (GRCm39)	V186M	probably damaging	Het
Alpk1	T	C	3: 127,466,991 (GRCm39)	Y1096C	probably damaging	Het
Ankrd29	A	C	18: 12,412,747 (GRCm39)	Y73*	probably null	Het
Asah2	A	T	19: 32,002,267 (GRCm39)	S292R	probably damaging	Het
Atp6v1b1	A	T	6: 83,729,377 (GRCm39)	T105S	probably damaging	Het
Axdnd1	T	A	1: 156,193,182 (GRCm39)		probably null	Het
Bub1b	T	G	2: 118,461,481 (GRCm39)	S678A	probably damaging	Het
Cdcp3	G	A	7: 130,872,328 (GRCm39)		probably benign	Het
Cenpq	T	A	17: 41,238,089 (GRCm39)	M142L	probably benign	Het
Ciz1	T	A	2: 32,260,063 (GRCm39)	V203E	possibly damaging	Het
Cmklr2	T	C	1: 63,222,434 (GRCm39)	E267G	probably damaging	Het
Cyp2c68	A	T	19: 39,729,452 (GRCm39)	S12T	probably benign	Het
Cyp4f18	C	A	8: 72,747,030 (GRCm39)	A322S	probably damaging	Het
Disp2	A	G	2: 118,622,624 (GRCm39)	S1119G	probably damaging	Het
Eif2ak4	C	T	2: 118,287,638 (GRCm39)	T1081M	probably damaging	Het
Faxc	A	G	4: 21,958,445 (GRCm39)	T201A	possibly damaging	Het
Fbxw14	A	G	9: 109,105,332 (GRCm39)	S278P	probably damaging	Het
Fpr1	G	T	17: 18,097,190 (GRCm39)	C266*	probably null	Het
Fsip2	T	C	2: 82,812,798 (GRCm39)	I3039T	probably benign	Het
Gas1	G	T	13: 60,324,186 (GRCm39)	S190R	possibly damaging	Het
Gemin2	A	G	12: 59,060,371 (GRCm39)	T37A	probably damaging	Het
Gm21370	T	C	13: 120,488,403 (GRCm39)	I49V	probably benign	Het
Gm8444	T	C	15: 81,727,807 (GRCm39)		probably benign	Het
Gria1	A	G	11: 57,128,936 (GRCm39)	D401G	possibly damaging	Het
Gstk1	G	A	6: 42,226,794 (GRCm39)	V187I	possibly damaging	Het
Hmcn1	T	C	1: 150,506,479 (GRCm39)	D3776G	probably damaging	Het
Itfg1	A	C	8: 86,563,094 (GRCm39)	V102G	probably damaging	Het
Kidins220	A	G	12: 25,101,307 (GRCm39)		probably null	Het
Kif13b	A	C	14: 64,973,664 (GRCm39)	D338A	probably damaging	Het
Mab21l2	T	C	3: 86,454,565 (GRCm39)	Y145C	probably damaging	Het
Magel2	A	G	7: 62,027,389 (GRCm39)	M98V	unknown	Het
Mdfic	T	C	6: 15,721,196 (GRCm39)		probably benign	Het
Minar1	A	G	9: 89,473,220 (GRCm39)	I897T	probably damaging	Het
Mlip	G	A	9: 77,137,764 (GRCm39)	S381L	probably damaging	Het
Mycbp2	A	G	14: 103,384,453 (GRCm39)	L3475P	probably damaging	Het
Myh14	G	A	7: 44,276,457 (GRCm39)	T1216I	probably damaging	Het
Nfatc2	T	A	2: 168,322,158 (GRCm39)	I914F	probably benign	Het
Nup58	T	C	14: 60,478,256 (GRCm39)		probably null	Het
Or10ag53	T	A	2: 87,083,042 (GRCm39)	S254T	probably damaging	Het
Or10al4	T	C	17: 38,037,032 (GRCm39)	L48P	probably damaging	Het
Or13a22	A	G	7: 140,072,529 (GRCm39)		probably benign	Het
Or2y13	G	T	11: 49,414,338 (GRCm39)		probably benign	Het
Or4l15	A	G	14: 50,198,526 (GRCm39)	M1T	probably null	Het
Or5p50	A	T	7: 107,421,781 (GRCm39)	N298K	probably benign	Het
Or7g20	A	C	9: 18,946,689 (GRCm39)	Q90P	probably benign	Het
Otx1	A	T	11: 21,949,406 (GRCm39)	L24H	probably damaging	Het
Oxr1	A	G	15: 41,689,315 (GRCm39)	Q513R	probably damaging	Het
Padi1	C	T	4: 140,554,276 (GRCm39)	V310M	probably damaging	Het
Pard3	T	C	8: 127,800,023 (GRCm39)	L11S	probably benign	Het
Pcdhb14	A	T	18: 37,581,497 (GRCm39)	D201V	probably damaging	Het
Pcdhb7	A	G	18: 37,475,622 (GRCm39)	R253G	probably benign	Het
Plxnb2	C	T	15: 89,051,461 (GRCm39)	D253N	probably damaging	Het
Ppp2cb	T	C	8: 34,105,502 (GRCm39)	S171P	probably damaging	Het
Prr5	C	T	15: 84,577,973 (GRCm39)	T94M	probably damaging	Het
Rp1	A	G	1: 4,420,092 (GRCm39)	F340S	probably damaging	Het
Rpa1	C	G	11: 75,201,062 (GRCm39)	G433A	probably benign	Het
Smg1	A	T	7: 117,788,386 (GRCm39)		probably benign	Het
Sry	C	G	Y: 2,662,975 (GRCm39)	Q228H	unknown	Homo
Svep1	C	T	4: 58,072,872 (GRCm39)	G2146R	probably damaging	Het
Tas2r106	A	G	6: 131,655,173 (GRCm39)	M226T	probably damaging	Het
Tbk1	T	C	10: 121,420,148 (GRCm39)	I14V	probably benign	Het
Tekt4	G	C	17: 25,691,197 (GRCm39)	V168L	probably damaging	Het
Tnfaip1	T	A	11: 78,418,372 (GRCm39)	T232S	probably damaging	Het
Trio	C	T	15: 27,744,038 (GRCm39)		probably null	Het
Ttn	T	A	2: 76,774,781 (GRCm39)	Y2133F	unknown	Het
Uap1l1	C	T	2: 25,252,741 (GRCm39)	R433H	probably damaging	Het
Ugt2b35	T	C	5: 87,155,181 (GRCm39)	F339L	probably damaging	Het
Unc5b	T	C	10: 60,608,003 (GRCm39)	Y699C	probably damaging	Het
Vcpip1	T	C	1: 9,795,005 (GRCm39)	H1122R	probably damaging	Het
Vmn2r91	T	C	17: 18,326,888 (GRCm39)	V391A	probably benign	Het
Vps13c	C	T	9: 67,822,939 (GRCm39)	R1327W	probably damaging	Het
Yes1	A	G	5: 32,802,385 (GRCm39)	Y100C	probably damaging	Het
Zfp407	A	T	18: 84,577,134 (GRCm39)	N1326K	possibly damaging	Het
Zfp518a	G	A	19: 40,903,890 (GRCm39)	C1273Y	probably benign	Het
Zfr	AGCAGCAGCAGCAGCTGCTGCTGCAGCAGCA	AGCAGCAGCA	15: 12,146,317 (GRCm39)		probably benign	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
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
R7060:Col2a1	UTSW	15	97,874,022 (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'- GGGGCCTTGATCACCTTTAAAG -3'
(R):5'- GGTATTCCTGGAGCCAAAGG -3'

Sequencing Primer
(F):5'- TTTAAAGCCAGCAATGCCAGGTTC -3'
(R):5'- AAGGATCCGCTGTAAGTATTGTCCC -3'

Posted On

2018-02-27