Mutagenetix > Incidental Mutation

Incidental Mutation 'FR4342:Col2a1'

511294

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

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

FR4342 ()

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

97873483-97902525 bp(-) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

C to A at 97886862 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000085693 (fasta)

Gene Model

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

AlphaFold

P28481

Predicted Effect

probably null
Transcript: ENSMUST00000023123

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483

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

probably null
Transcript: ENSMUST00000088355

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483

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

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.7%
3x: 99.4%
10x: 97.8%
20x: 93.8%

Validation Efficiency

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: 108 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2810004N23Rik	TT	TTATGT	8: 125,566,572 (GRCm39)		probably null	Homo
4930433I11Rik	AACC	A	7: 40,642,479 (GRCm39)		probably benign	Het
7530416G11Rik	T	A	15: 85,378,508 (GRCm39)	E45V	unknown	Homo
Ankrd35	TCCCC	TCCC	3: 96,590,831 (GRCm39)		probably null	Het
Anxa2	CCC	CCCACC	9: 69,387,487 (GRCm39)		probably benign	Het
Anxa2	C	CCCA	9: 69,387,492 (GRCm39)		probably benign	Het
Apc	CAATAAAGC	CAATAAAGCAAATAAAGC	18: 34,415,052 (GRCm39)		probably benign	Homo
Arrb2	C	T	11: 70,329,497 (GRCm39)	T269M	probably damaging	Homo
Bcas3	G	A	11: 85,400,323 (GRCm39)	V431I	probably benign	Homo
Begain	CCCCGCC	CCCCGCCCCCGCC	12: 108,999,344 (GRCm39)		probably benign	Homo
Catsper2	TCA	TCAACA	2: 121,228,274 (GRCm39)		probably benign	Het
Ccdc121	GAGAAG	GAG	5: 31,644,717 (GRCm39)		probably benign	Homo
Cd164	G	T	10: 41,397,922 (GRCm39)	A59S	probably benign	Homo
Cd22	C	T	7: 30,577,507 (GRCm39)	R2H	possibly damaging	Homo
Cimip2b	CAGAG	CAG	4: 43,427,384 (GRCm39)		probably null	Homo
Cluh	GAGCCT	GAGCCTCAGCCT	11: 74,560,350 (GRCm39)		probably benign	Het
Cluh	GCCTGA	GCCTGAACCTGA	11: 74,560,352 (GRCm39)		probably benign	Het
Cntnap1	AGCCCC	AGCCCCCGCCCC	11: 101,080,401 (GRCm39)		probably benign	Het
Col6a5	A	T	9: 105,811,373 (GRCm39)	N715K	unknown	Homo
Cpeb4	T	TGA	11: 31,877,638 (GRCm39)		probably benign	Homo
Dbr1	AGGAGG	AGGAGGGGGAGG	9: 99,465,733 (GRCm39)		probably benign	Het
Defa29	C	G	8: 21,816,160 (GRCm39)	R69P	probably benign	Het
Dhx8	CG	CGAGAACGG	11: 101,629,032 (GRCm39)		probably null	Het
Dnaaf9	TCC	TCCCCC	2: 130,612,662 (GRCm39)		probably benign	Het
Dnah12	G	T	14: 26,571,342 (GRCm39)	G2817V	probably damaging	Homo
Dthd1	C	CTTA	5: 63,000,369 (GRCm39)		probably benign	Homo
E4f1	GC	GCCCC	17: 24,674,171 (GRCm39)		probably benign	Het
F830016B08Rik	A	ACAG	18: 60,433,013 (GRCm39)		probably benign	Homo
Fbrsl1	GTGTGTGTGCTGGTGCGTGTGCTGGTG	GTGTGTGTGCTGGTGTGTGTGCTGGTGCGTGTGCTGGTG	5: 110,525,991 (GRCm39)		probably benign	Het
Fbxo22	A	C	9: 55,128,354 (GRCm39)		probably null	Het
Flg	G	A	3: 93,197,820 (GRCm39)		probably benign	Het
Fmn1	TCC	TCCTCCACC	2: 113,356,128 (GRCm39)		probably benign	Homo
Frmpd2	G	T	14: 33,232,978 (GRCm39)	L399F	probably damaging	Homo
Gbp2b	A	G	3: 142,309,413 (GRCm39)	I175V	probably benign	Het
Gjc2	T	TCCCG	11: 59,073,569 (GRCm39)		probably benign	Homo
Gm14496	A	C	2: 181,637,699 (GRCm39)	K258Q	probably benign	Het
Gm4340	CAGAAG	CAGAAGAAG	10: 104,031,960 (GRCm39)		probably benign	Het
Gm4340	CAGAAG	CAGAAGAAG	10: 104,031,927 (GRCm39)		probably benign	Het
Gpatch11	AGAGGA	AGAGGATGAGGA	17: 79,149,607 (GRCm39)		probably benign	Het
H1f6	TGTGG	TG	13: 23,879,896 (GRCm39)		probably benign	Homo
H2-Q4	G	A	17: 35,599,381 (GRCm39)	D155N	probably damaging	Homo
Hoxa3	G	GCTT	6: 52,147,110 (GRCm39)		probably benign	Homo
Ifi208	ATGGTG	ATG	1: 173,505,264 (GRCm39)		probably benign	Homo
Ighv5-9	C	T	12: 113,625,497 (GRCm39)	S82N	probably benign	Homo
Klra10	G	A	6: 130,249,710 (GRCm39)	R192C	probably benign	Het
Kmt2b	TCCTCC	TCCTCCCCCTCC	7: 30,285,800 (GRCm39)		probably benign	Het
Krt10	CGCC	CGCCGCC	11: 99,277,025 (GRCm39)		probably benign	Het
Krt10	ACC	ACCCCC	11: 99,277,029 (GRCm39)		probably benign	Homo
Lce1m	CGCTGCTGCTGCCACAGCA	C	3: 92,925,554 (GRCm39)		probably benign	Het
Mak16	T	G,A	8: 31,651,777 (GRCm39)	E203D	probably benign	Homo
Med12l	AGC	AGCGGC	3: 59,183,409 (GRCm39)		probably benign	Het
Med12l	AGCGGC	AGCGGCGGC	3: 59,183,415 (GRCm39)		probably benign	Het
Mn1	AGC	AGCGGC	5: 111,567,572 (GRCm39)		probably benign	Het
Nacad	TC	TCAGGGGC	11: 6,549,762 (GRCm39)		probably benign	Het
Naip1	C	T	13: 100,561,979 (GRCm39)	R1062K	probably benign	Het
Ndel1	G	A	11: 68,724,235 (GRCm39)	P246L	probably damaging	Het
Nelfe	AC	ACAAAGAGCGGGATCGAGACAGAGCC	17: 35,073,065 (GRCm39)		probably benign	Het
Or51q1	TCC	TCCC	7: 103,629,110 (GRCm39)		probably null	Het
Or5p70	A	G	7: 107,995,100 (GRCm39)	T258A	probably benign	Het
Or5p70	G	A	7: 107,995,105 (GRCm39)	M259I	probably benign	Het
P4ha2	GTGTTGCTG	GTG	11: 54,001,077 (GRCm39)		probably benign	Homo
Pde3b	GGTGGTGGTG	GGTGGTGGTGGTG	7: 114,134,010 (GRCm39)		probably benign	Homo
Pdik1l	ACCACC	ACCACCCCCACC	4: 134,006,820 (GRCm39)		probably benign	Homo
Phaf1	G	A	8: 105,967,730 (GRCm39)	G207E	probably benign	Homo
Plekhs1	AGAC	AGACCTCCCCCGCGAC	19: 56,468,293 (GRCm39)		probably benign	Homo
Plekhs1	TCCAGAC	TCCAGACCTCCCCCCAGAC	19: 56,468,290 (GRCm39)		probably benign	Homo
Pramel16	AAGAG	AAG	4: 143,676,327 (GRCm39)		probably null	Het
Pramel16	G	A	4: 143,676,312 (GRCm39)	T264M	probably damaging	Het
Pramel27	AA	AATA	4: 143,578,213 (GRCm39)		probably null	Homo
Prkn	G	A	17: 12,073,650 (GRCm39)	V323M	probably damaging	Homo
Ptms	TCT	TCTCCT	6: 124,891,417 (GRCm39)		probably benign	Homo
Raet1d	A	G	10: 22,247,458 (GRCm39)	Q178R	probably benign	Het
Rtbdn	AGCG	AGCGCCGGCG	8: 85,682,797 (GRCm39)		probably benign	Het
Rtbdn	GC	GCAGCGCC	8: 85,682,807 (GRCm39)		probably benign	Het
Semp2l2a	G	C	8: 13,887,613 (GRCm39)	H159Q	probably benign	Het
Serac1	T	A	17: 6,121,083 (GRCm39)	K70N	probably damaging	Homo
Sfswap	CCCACTC	CCCACTCAGACCACTC	5: 129,646,821 (GRCm39)		probably benign	Homo
Sp110	ACT	ACTGCT	1: 85,515,209 (GRCm39)		probably benign	Het
Spaca1	GCTCTC	GCTCTCACTCTC	4: 34,049,838 (GRCm39)		probably benign	Het
Spag17	GGA	GGATGA	3: 99,963,565 (GRCm39)		probably benign	Het
Spag17	GGAGGAGGA	GGAGGAGGAGGA	3: 99,963,568 (GRCm39)		probably benign	Homo
Speer4a1	C	A	5: 26,241,746 (GRCm39)	E127*	probably null	Het
Sry	GGT	GGTTGT	Y: 2,662,836 (GRCm39)		probably benign	Het
Sry	TGG	TGGGGG	Y: 2,662,835 (GRCm39)		probably benign	Het
Sry	CTGCTGGTG	CTG	Y: 2,663,146 (GRCm39)		probably benign	Het
Sry	GGT	GGTAGT	Y: 2,662,839 (GRCm39)		probably benign	Homo
Tdpoz3	C	T	3: 93,733,819 (GRCm39)	P165S	probably benign	Het
Tdpoz4	GAA	GA	3: 93,704,187 (GRCm39)		probably null	Het
Tert	AGGCC	AGGCCAAGGGGGCC	13: 73,796,419 (GRCm39)		probably benign	Homo
Tmbim7	C	T	5: 3,720,064 (GRCm39)	R100C	possibly damaging	Homo
Tnfrsf9	CT	CTGAT	4: 151,018,851 (GRCm39)		probably benign	Homo
Tob1	AGC	AGCCGC	11: 94,105,298 (GRCm39)		probably benign	Het
Trav6n-5	GCTT	G	14: 53,342,369 (GRCm39)		probably benign	Homo
Triobp	G	GTCA	15: 78,877,592 (GRCm39)		probably benign	Homo
Tsen2	AGG	AGGTGG	6: 115,537,033 (GRCm39)		probably benign	Het
Ubtf	TCC	TCCGCC	11: 102,197,782 (GRCm39)		probably benign	Het
Ubtf	TC	TCCCC	11: 102,197,785 (GRCm39)		probably benign	Het
Vmn2r125	G	A	4: 156,703,260 (GRCm39)	V213I	probably benign	Het
Vmn2r87	C	T	10: 130,314,583 (GRCm39)	M334I	probably benign	Homo
Zdhhc16	G	A	19: 41,930,588 (GRCm39)		probably benign	Het
Zfp28	G	A	7: 6,397,862 (GRCm39)	G766R	probably damaging	Het
Zfp335	GTCGTC	GTCGTCGTC	2: 164,749,385 (GRCm39)		probably benign	Het
Zfp335	C	CCCC	2: 164,749,397 (GRCm39)		probably benign	Het
Zfp428	G	A	7: 24,214,506 (GRCm39)	D41N	probably damaging	Homo
Zfp429	A	T	13: 67,544,769 (GRCm39)	F48Y	probably benign	Het
Zfp598	CCACC	CCACCCACACC	17: 24,899,754 (GRCm39)		probably benign	Het
Zfp93	G	A	7: 23,975,011 (GRCm39)	R332H	possibly damaging	Het
Zpld2	G	GCTC	4: 133,929,942 (GRCm39)		probably benign	Homo

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
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
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'- ACCAGTTGCACCTTGAGGAC -3'
(R):5'- CACTAAATGGTCATGCTGGC -3'

Sequencing Primer
(F):5'- ACCTTGAGGACCGGGAG -3'
(R):5'- GGTCATGCTGGCCAAACAC -3'

Posted On

2018-04-05