Mutagenetix > Incidental Mutations

Incidental Mutation 'LCD18:Col2a1'

478065

Institutional Source

Beutler Lab

Gene Symbol

Col2a1

Ensembl Gene

ENSMUSG00000022483

Gene Name

collagen, type II, alpha 1

Synonyms

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

Accession Numbers

Is this an essential gene?

Essential (E-score: 1.000) question?

Stock #

LCD18 (G1)

Quality Score

999

Status

Not validated

Chromosome

Chromosomal Location

97975602-98004695 bp(-) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

C to A at 97988981 bp

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000085693 (fasta)

Gene Model

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

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: 0.0%
3x: 0.0%
10x: 0.0%
20x: 0.0%

Validation Efficiency

88% (169/191)

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: 113 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700007G11Rik	G	A	5: 98,707,508		probably benign	Het
4930548H24Rik	GAGAAG	GAG	5: 31,487,373		probably benign	Het
9530077C05Rik	N		9: 22,442,083		probably benign	Het
A330008L17Rik	A	G	8: 99,723,425		noncoding transcript	Het
Aaed1	G	A	13: 64,287,285		probably benign	Het
Aff2	C	A	X: 69,747,535		probably benign	Het
Aldh1a1	C	A	19: 20,626,646		probably benign	Het
Anxa7	C	T	14: 20,469,411	G113E	probably damaging	Het
Apba2	A	T	7: 64,622,160		probably benign	Het
Apc2	G	C	10: 80,299,974		probably benign	Het
App	C	G	16: 85,025,412		probably benign	Het
Asic2	C	A	11: 80,985,744		probably benign	Het
Btk	T	C	X: 134,578,825		probably benign	Het
C530008M17Rik	GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	GGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	5: 76,658,742		probably benign	Het
Car12	C	A	9: 66,761,676		probably benign	Het
Ccdc191	G	A	16: 43,921,801		probably benign	Het
Ccdc34	N		2: 110,016,318		probably benign	Het
Cd164	G	T	10: 41,521,926	A59S	probably benign	Het
Cd22	C	T	7: 30,878,082	R2H	possibly damaging	Het
Cdv3	A	T	9: 103,365,343		probably benign	Het
Cdv3	C	A	9: 103,365,354		probably benign	Het
Celf2	N		2: 6,779,076		probably benign	Het
Clec18a	C	A	8: 111,076,136		probably benign	Het
Cnpy3	GGATGGAT	GGATAGATAGATAGATAGATGGAT	17: 46,737,536		probably benign	Het
Cntn4	A	G	6: 106,553,940		probably benign	Het
Cntnap5c	G	C	17: 58,162,160		probably benign	Het
Cpne3	G	T	4: 19,563,382		probably benign	Het
Dab1	T	G	4: 104,046,572		probably benign	Het
Dapp1	G	A	3: 137,939,400		probably benign	Het
Dcc	G	A	18: 72,297,447		probably benign	Het
Dcun1d1	GAAAAAAAAA	GAAAAAAAAAA	3: 35,938,005		probably benign	Het
Dennd1b	G	A	1: 139,114,764		probably benign	Het
Dhdds	TAA	TA	4: 133,970,363		probably benign	Het
Dnah12	G	T	14: 26,849,385	G2817V	probably damaging	Het
Dnm3	CATATATATATATATATATATATA	CATATATATATATATATATATA	1: 162,406,561		probably benign	Het
Dock10	N		1: 80,716,623		probably benign	Het
Dusp10	G	T	1: 184,037,056	C73F	probably damaging	Het
Fgf20	A	C	8: 40,292,318		probably benign	Het
Ftsj3	G	T	11: 106,250,059		probably benign	Het
Gls	T	G	1: 52,183,367		probably benign	Het
Gm12130	T	C	11: 38,506,923		noncoding transcript	Het
Gm12394	T	C	4: 42,792,885	T416A	probably benign	Het
Gm14936	G	A	X: 112,998,750		noncoding transcript	Het
Gm16630	C	T	6: 48,141,269		noncoding transcript	Het
Gm22194	AGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	AGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG	10: 11,940,963		noncoding transcript	Het
Gm26917	C	G	17: 39,843,971		noncoding transcript	Het
Gm35048	GACACACACACACACACACACACACACACACACACACAC	GACACACACACACACACACACACACACACACACACAC	1: 90,521,526		noncoding transcript	Het
Gm37311	G	A	16: 77,618,281		noncoding transcript	Het
Gm37928	AACACACACACACACACACACACACACACACACA	AACACACACACACACACACACACACACACACACACA	3: 118,534,557		noncoding transcript	Het
Gm42418	T	C	17: 39,848,555		noncoding transcript	Het
Gm4302	T	C	10: 100,341,444	W197R	probably benign	Het
Gm5615	T	C	9: 36,533,553		probably benign	Het
H2-Q4	G	A	17: 35,380,405	D155N	probably damaging	Het
H2-T23	T	C	17: 36,031,216		probably benign	Het
Hgs	CTTTTTTT	CTTTTTT	11: 120,469,578		probably benign	Het
Ighv5-9	C	T	12: 113,661,877	S82N	probably benign	Het
Il1rap	C	A	16: 26,631,593		probably benign	Het
Inhbc	N		10: 127,367,140		probably benign	Het
Inpp4b	C	T	8: 81,693,010		probably benign	Het
Kars	N		8: 111,993,708		probably benign	Het
Kcng4	G	T	8: 119,633,519	Y39*	probably null	Het
Kcnh7	A	G	2: 63,049,799		probably benign	Het
Klhl1	G	C	14: 96,317,730		probably benign	Het
Lrch1	C	T	14: 74,905,021		probably benign	Het
Lrp1b	G	C	2: 42,237,562		probably benign	Het
Lsm8	G	A	6: 18,844,316		probably benign	Het
Lsm8	G	A	6: 18,854,321		probably benign	Het
Magi2	T	C	5: 19,954,511		probably benign	Het
Marc2	TAGGCAGCCAATCAGAGCACTGCCTCTCAGCGCCAGGCAGCCAATCAGAGCACTGCCTCTCAGCGCCAGGCA	TAGGCAGCCAATCAGAGCACTGCCTCTCAGCGCCAGGCA	1: 184,822,788		probably benign	Het
Mef2c	G	A	13: 83,605,823		probably benign	Het
Mei4	A	G	9: 82,186,959		probably benign	Het
Mid1	T	A	X: 170,005,564		probably benign	Het
Mndal	G	C	1: 173,880,218		probably benign	Het
Mpped2	C	A	2: 106,721,428		probably benign	Het
Mtf1	A	G	4: 124,829,316		probably benign	Het
Mxd1	T	C	6: 86,667,406		probably benign	Het
Nbea	G	T	3: 55,701,527		probably benign	Het
Ncor1	N		11: 62,419,782		probably benign	Het
Nox4	A	G	7: 87,243,067		probably benign	Het
Ocln	C	T	13: 100,520,567		probably benign	Het
Ofcc1	G	A	13: 40,092,967		probably benign	Het
Olfr313	T	A	11: 58,817,440	V144D	possibly damaging	Het
Paics	N		5: 76,956,744		probably null	Het
Paqr8	G	T	1: 20,914,658		probably benign	Het
Pdss1	C	T	2: 22,900,968		probably benign	Het
Piezo1	G	A	8: 122,495,569	R503W	probably damaging	Het
Pkhd1	G	A	1: 20,611,414		probably benign	Het
Ppp1r3f	C	A	X: 7,560,336	G562V	probably damaging	Het
Prr16	C	T	18: 51,200,324		probably benign	Het
Prss38	T	G	11: 59,375,641		probably benign	Het
Ptprk	T	C	10: 28,574,987		probably benign	Het
Pum1	N		4: 130,730,549		probably benign	Het
Rabgef1	N		5: 130,187,586		probably null	Het
Rgs16	G	A	1: 153,744,230		probably benign	Het
Riok3	G	T	18: 12,129,982		probably benign	Het
Robo2	N		16: 74,055,954		probably benign	Het
Rps6ka3	A	G	X: 159,279,215		probably benign	Het
Rptn	T	A	3: 93,397,541	L727Q	probably benign	Het
Slc25a46	C	A	18: 31,597,313		probably benign	Het
Spsb1	C	T	4: 149,952,486		probably benign	Het
Tbc1d19	A	C	5: 53,816,709		probably benign	Het
Trav7-4	C	T	14: 53,461,518	L41F	probably benign	Het
Trip12	N		1: 84,754,482		probably benign	Het
Ttc13	G	A	8: 124,675,866		probably benign	Het
Ttll6	C	T	11: 96,155,258		probably benign	Het
Unc5b	C	G	10: 60,786,171		probably benign	Het
Vmn2r87	C	T	10: 130,478,714	M334I	probably benign	Het
Vps13b	G	T	15: 35,846,957	A2629S	probably damaging	Het
Wars2	N		3: 99,214,774		probably null	Het
Zdhhc3	AACACACACACACACACACACACACACACACAC	AACACACACACACACACACACACACACACACACAC	9: 123,083,022		probably benign	Het
Zfp26	C	A	9: 20,438,546	A241S	probably benign	Het
Zfp442	C	T	2: 150,419,848		probably benign	Het
Zfp808	C	T	13: 62,166,651		probably benign	Het

Other mutations in Col2a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01025:Col2a1	APN	15	97976173	missense	unknown
IGL01286:Col2a1	APN	15	97994878	missense	unknown
IGL01369:Col2a1	APN	15	97977826	missense	unknown
IGL01747:Col2a1	APN	15	97991392	splice site	probably benign
IGL02086:Col2a1	APN	15	97986737	splice site	probably null
IGL02549:Col2a1	APN	15	97977799	missense	unknown
IGL03289:Col2a1	APN	15	97980881	missense	unknown
IGL03369:Col2a1	APN	15	97982042	missense	unknown
Foreseen	UTSW	15	97976793	missense	unknown
FR4304:Col2a1	UTSW	15	97988981	splice site	probably null
FR4340:Col2a1	UTSW	15	97988981	splice site	probably null
FR4342:Col2a1	UTSW	15	97988981	splice site	probably null
FR4589:Col2a1	UTSW	15	97988981	splice site	probably null
R0124:Col2a1	UTSW	15	97998862	missense	unknown
R0227:Col2a1	UTSW	15	97976755	missense	unknown
R0690:Col2a1	UTSW	15	97980192	missense	unknown
R1434:Col2a1	UTSW	15	97979651	missense	probably damaging	0.96
R1473:Col2a1	UTSW	15	97982908	splice site	probably benign
R1577:Col2a1	UTSW	15	97979202	missense	probably damaging	1.00
R1598:Col2a1	UTSW	15	97979250	missense	probably damaging	0.99
R1837:Col2a1	UTSW	15	97996641	splice site	probably benign
R2153:Col2a1	UTSW	15	97987580	missense	unknown
R2965:Col2a1	UTSW	15	97976095	missense	unknown
R2966:Col2a1	UTSW	15	97976095	missense	unknown
R3710:Col2a1	UTSW	15	97990907	splice site	probably benign
R3838:Col2a1	UTSW	15	97988976	missense	unknown
R3838:Col2a1	UTSW	15	98000581	intron	probably benign
R4112:Col2a1	UTSW	15	97983701	missense	probably benign	0.18
R4417:Col2a1	UTSW	15	97998585	missense	unknown
R4656:Col2a1	UTSW	15	97976176	missense	unknown
R4960:Col2a1	UTSW	15	97976149	missense	unknown
R5008:Col2a1	UTSW	15	97979669	missense	probably benign	0.28
R5435:Col2a1	UTSW	15	98000510	intron	probably benign
R5473:Col2a1	UTSW	15	97987489	missense	unknown
R6042:Col2a1	UTSW	15	98000570	intron	probably benign
R6118:Col2a1	UTSW	15	97998567	missense	unknown
R6183:Col2a1	UTSW	15	97988790	missense	unknown
R6187:Col2a1	UTSW	15	97988790	missense	unknown
R6401:Col2a1	UTSW	15	97985892	missense	unknown
R6550:Col2a1	UTSW	15	97976793	missense	unknown
R6568:Col2a1	UTSW	15	97977276	missense	unknown
R6988:Col2a1	UTSW	15	98004454	missense	unknown
R7060:Col2a1	UTSW	15	97976141	missense	unknown
R7069:Col2a1	UTSW	15	97998588	missense	unknown
R7167:Col2a1	UTSW	15	98000456	missense	unknown
R7294:Col2a1	UTSW	15	97987287	splice site	probably null
R7392:Col2a1	UTSW	15	97980151	nonsense	probably null
R7491:Col2a1	UTSW	15	97976159	missense	not run
R7583:Col2a1	UTSW	15	97976184	missense	unknown
R7665:Col2a1	UTSW	15	97976700	missense	unknown
R7872:Col2a1	UTSW	15	98000577	nonsense	probably null
R8177:Col2a1	UTSW	15	97976773	missense	unknown
R8306:Col2a1	UTSW	15	97990968	critical splice acceptor site	probably null
Z1177:Col2a1	UTSW	15	97983973	missense	probably damaging	1.00
Z1177:Col2a1	UTSW	15	97998345	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ACCAGTTGCACCTTGAGGAC -3'
(R):5'- TCATGCTGGCCAAACACCTC -3'

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

Posted On

2017-05-17