Mutagenetix > Incidental Mutation

Incidental Mutation 'R3838:Col2a1'

277023

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

MMRRC Submission

040779-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R3838 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

97975602-98004695 bp(-) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 97988976 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 345 (D345G)

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: D413G

SMART Domains

Protein: ENSMUSP00000023123
Gene: ENSMUSG00000022483
AA Change: D413G

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: D345G

SMART Domains

Protein: ENSMUSP00000085693
Gene: ENSMUSG00000022483
AA Change: D345G

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: 99.3%
3x: 98.8%
10x: 97.8%
20x: 96.4%

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: 57 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700042G07Rik	A	G	4: 116,173,521	T41A	probably benign	Het
4930486L24Rik	A	G	13: 60,845,227	Y213H	probably damaging	Het
Alg8	C	T	7: 97,388,545	H379Y	probably damaging	Het
Arhgef25	T	C	10: 127,189,736	T12A	probably benign	Het
Arid4a	A	G	12: 71,075,785	E980G	possibly damaging	Het
Aspm	C	T	1: 139,478,054	H1560Y	probably benign	Het
Atg10	A	T	13: 90,937,380	I150K	probably damaging	Het
Bud13	A	C	9: 46,290,192	Q387P	possibly damaging	Het
Champ1	A	G	8: 13,879,939	Y699C	probably damaging	Het
Clstn1	A	G	4: 149,638,333	E476G	probably damaging	Het
Col9a2	C	G	4: 121,054,258	R599G	probably damaging	Het
Dnajb2	G	A	1: 75,241,480		probably null	Het
Dock4	G	T	12: 40,794,624		probably null	Het
Epx	A	T	11: 87,874,830	L101Q	probably damaging	Het
F13a1	A	T	13: 37,047,424	N21K	probably damaging	Het
Fam13c	C	T	10: 70,542,648	S336L	probably damaging	Het
Fam35a	T	C	14: 34,245,368	D77G	probably benign	Het
Foxj3	T	A	4: 119,616,624	H215Q	possibly damaging	Het
Gcnt4	A	T	13: 96,947,014	R273*	probably null	Het
Gpam	T	C	19: 55,080,458	N450S	probably benign	Het
Hivep2	C	A	10: 14,128,969	T437K	probably benign	Het
Hmcn2	T	C	2: 31,413,407	L3020P	probably damaging	Het
Hmgcr	A	G	13: 96,659,089	I324T	probably benign	Het
Ighmbp2	T	C	19: 3,271,658	Y367C	probably benign	Het
Lrrc14b	A	G	13: 74,363,545	C139R	possibly damaging	Het
Lsamp	A	T	16: 42,134,312	E174V	possibly damaging	Het
Mid1ip1	T	C	X: 10,718,381	V51A	possibly damaging	Het
Mrc2	G	A	11: 105,348,431		probably null	Het
Msn	C	A	X: 96,160,199	Q303K	probably damaging	Het
Myh7b	A	G	2: 155,632,989	K1816E	probably damaging	Het
Nap1l1	T	A	10: 111,495,322		probably null	Het
Nme2	T	A	11: 93,949,977	E252D	probably benign	Het
Ntpcr	G	A	8: 125,737,372	V79M	probably damaging	Het
Ogdh	C	T	11: 6,338,627	R235*	probably null	Het
Olfr1490	A	G	19: 13,654,957	D176G	probably benign	Het
Olfr825	C	A	10: 130,162,406	E307*	probably null	Het
Olfr959	A	G	9: 39,572,971	V96A	probably benign	Het
Pcdh20	T	C	14: 88,468,463	N467S	probably benign	Het
Pkhd1	G	A	1: 20,534,629	T1154I	possibly damaging	Het
Polq	G	T	16: 37,078,349	R2157I	probably damaging	Het
Reep6	C	A	10: 80,335,889	A533E	probably damaging	Het
Senp2	T	C	16: 22,009,735	S32P	probably damaging	Het
Sept11	T	A	5: 93,148,399	I52N	probably damaging	Het
Slc17a4	C	T	13: 23,901,769	R387H	probably benign	Het
Spdye4b	C	T	5: 143,192,329	T11I	probably benign	Het
Srrt	C	T	5: 137,302,125		probably null	Het
Sspo	T	A	6: 48,480,820	C3085S	probably damaging	Het
Stim1	C	T	7: 102,411,296	T182I	possibly damaging	Het
Thbs2	C	A	17: 14,687,851	V217L	probably benign	Het
Thpo	G	A	16: 20,728,748	R38C	probably damaging	Het
Tmem210	A	G	2: 25,288,432	E35G	possibly damaging	Het
Trim12c	T	A	7: 104,340,868		probably benign	Het
Tvp23b	A	G	11: 62,883,629	H33R	possibly damaging	Het
Usp14	A	G	18: 10,024,532		probably null	Het
Vmn2r73	A	G	7: 85,858,050	W685R	probably benign	Het
Zfp618	G	A	4: 63,133,564	A861T	probably benign	Het
Zfp715	A	G	7: 43,299,756	V260A	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
LCD18: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	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
R9343:Col2a1	UTSW	15	97979894	missense	probably damaging	0.99
R9458:Col2a1	UTSW	15	97978361	missense	unknown
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'- ACTAAATGGTCATGCTGGCC -3'

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

Posted On

2015-04-06