Mutagenetix > Incidental Mutation

Incidental Mutation 'R0090:Col9a1'

20105

Institutional Source

Beutler Lab

Gene Symbol

Col9a1

Ensembl Gene

ENSMUSG00000026147

Gene Name

collagen, type IX, alpha 1

Synonyms

Col9a-1

MMRRC Submission

038377-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.121) question?

Stock #

R0090 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24216691-24291765 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

T to A at 24262643 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000085687 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000054588] [ENSMUST00000054588] [ENSMUST00000054588] [ENSMUST00000088349] [ENSMUST00000088349] [ENSMUST00000088349]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000054588

SMART Domains

Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TSPN	50	244	5.73e-78	SMART
Pfam:Collagen	266	326	2e-11	PFAM
Pfam:Collagen	308	358	3.5e-9	PFAM
Pfam:Collagen	357	409	1.2e-8	PFAM
Pfam:Collagen	415	472	7.8e-11	PFAM
Pfam:Collagen	454	515	2.9e-11	PFAM
Pfam:Collagen	592	667	3.9e-8	PFAM
Pfam:Collagen	646	716	1.7e-9	PFAM
Pfam:Collagen	697	760	1.6e-10	PFAM
Pfam:Collagen	785	848	3.1e-11	PFAM
low complexity region	878	899	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000054588

SMART Domains

Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TSPN	50	244	5.73e-78	SMART
Pfam:Collagen	266	326	2e-11	PFAM
Pfam:Collagen	308	358	3.5e-9	PFAM
Pfam:Collagen	357	409	1.2e-8	PFAM
Pfam:Collagen	415	472	7.8e-11	PFAM
Pfam:Collagen	454	515	2.9e-11	PFAM
Pfam:Collagen	592	667	3.9e-8	PFAM
Pfam:Collagen	646	716	1.7e-9	PFAM
Pfam:Collagen	697	760	1.6e-10	PFAM
Pfam:Collagen	785	848	3.1e-11	PFAM
low complexity region	878	899	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000054588

SMART Domains

Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TSPN	50	244	5.73e-78	SMART
Pfam:Collagen	266	326	2e-11	PFAM
Pfam:Collagen	308	358	3.5e-9	PFAM
Pfam:Collagen	357	409	1.2e-8	PFAM
Pfam:Collagen	415	472	7.8e-11	PFAM
Pfam:Collagen	454	515	2.9e-11	PFAM
Pfam:Collagen	592	667	3.9e-8	PFAM
Pfam:Collagen	646	716	1.7e-9	PFAM
Pfam:Collagen	697	760	1.6e-10	PFAM
Pfam:Collagen	785	848	3.1e-11	PFAM
low complexity region	878	899	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000088349

SMART Domains

Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
low complexity region	7	22	N/A	INTRINSIC
Pfam:Collagen	24	85	1.5e-11	PFAM
Pfam:Collagen	66	117	2.7e-9	PFAM
Pfam:Collagen	115	168	2.8e-8	PFAM
Pfam:Collagen	174	231	5.5e-11	PFAM
Pfam:Collagen	213	274	1.9e-11	PFAM
low complexity region	353	391	N/A	INTRINSIC
Pfam:Collagen	405	479	1.3e-9	PFAM
Pfam:Collagen	456	519	1e-10	PFAM
Pfam:Collagen	544	607	2.4e-11	PFAM
low complexity region	637	658	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000088349

SMART Domains

Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
low complexity region	7	22	N/A	INTRINSIC
Pfam:Collagen	24	85	1.5e-11	PFAM
Pfam:Collagen	66	117	2.7e-9	PFAM
Pfam:Collagen	115	168	2.8e-8	PFAM
Pfam:Collagen	174	231	5.5e-11	PFAM
Pfam:Collagen	213	274	1.9e-11	PFAM
low complexity region	353	391	N/A	INTRINSIC
Pfam:Collagen	405	479	1.3e-9	PFAM
Pfam:Collagen	456	519	1e-10	PFAM
Pfam:Collagen	544	607	2.4e-11	PFAM
low complexity region	637	658	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000088349

SMART Domains

Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
low complexity region	7	22	N/A	INTRINSIC
Pfam:Collagen	24	85	1.5e-11	PFAM
Pfam:Collagen	66	117	2.7e-9	PFAM
Pfam:Collagen	115	168	2.8e-8	PFAM
Pfam:Collagen	174	231	5.5e-11	PFAM
Pfam:Collagen	213	274	1.9e-11	PFAM
low complexity region	353	391	N/A	INTRINSIC
Pfam:Collagen	405	479	1.3e-9	PFAM
Pfam:Collagen	456	519	1e-10	PFAM
Pfam:Collagen	544	607	2.4e-11	PFAM
low complexity region	637	658	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000124600

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 98.9%
3x: 98.0%
10x: 95.7%
20x: 91.4%

Validation Efficiency

99% (90/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of the three alpha chains of type IX collagen, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted mutation show no conspicuous skeletal abnormalities at birth but develop early-onset degenerative joint disease resembling osteoarthritis as well as progressive hearing loss; restoration and remodeling of trabecular bone is perturbed with minimal effects on cortical bone. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 89 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2010315B03Rik	T	C	9: 124,057,789 (GRCm39)		probably benign	Het
4933427I04Rik	A	G	4: 123,754,775 (GRCm39)	T230A	possibly damaging	Het
Acsm1	T	C	7: 119,261,412 (GRCm39)		probably benign	Het
Acta1	T	C	8: 124,620,396 (GRCm39)	N14S	probably damaging	Het
Aff4	A	G	11: 53,283,609 (GRCm39)	T362A	probably benign	Het
Aggf1	A	G	13: 95,501,467 (GRCm39)	I305T	probably benign	Het
Ap4b1	A	G	3: 103,727,745 (GRCm39)	D325G	possibly damaging	Het
Ap4e1	C	T	2: 126,906,905 (GRCm39)	T1055I	possibly damaging	Het
Arhgef2	A	T	3: 88,546,655 (GRCm39)	Q496L	probably damaging	Het
Arhgef28	A	G	13: 98,211,618 (GRCm39)	F122L	probably damaging	Het
Baiap3	G	A	17: 25,469,044 (GRCm39)		probably benign	Het
Casp8ap2	T	A	4: 32,640,327 (GRCm39)	H460Q	probably damaging	Het
Casz1	A	G	4: 149,017,868 (GRCm39)	T386A	probably benign	Het
Cd53	A	T	3: 106,674,725 (GRCm39)	V114E	possibly damaging	Het
Celsr2	A	G	3: 108,300,643 (GRCm39)		probably benign	Het
Cfap300	T	A	9: 8,027,184 (GRCm39)	N118I	probably benign	Het
Chaf1b	G	T	16: 93,684,012 (GRCm39)	A88S	possibly damaging	Het
Cldn10	A	T	14: 119,111,612 (GRCm39)	Y194F	probably damaging	Het
Clec2e	A	C	6: 129,072,181 (GRCm39)		probably null	Het
Cmpk2	A	T	12: 26,528,021 (GRCm39)	T413S	probably benign	Het
Dchs1	G	T	7: 105,405,139 (GRCm39)	Q2468K	probably benign	Het
Ddx60	A	G	8: 62,395,327 (GRCm39)	D88G	probably damaging	Het
Dnah8	A	G	17: 31,003,064 (GRCm39)	R3588G	probably benign	Het
Ect2	T	C	3: 27,169,625 (GRCm39)	T774A	probably benign	Het
Ect2	C	T	3: 27,192,651 (GRCm39)	E431K	probably null	Het
Ern1	A	G	11: 106,296,649 (GRCm39)	V767A	probably damaging	Het
Fbln1	A	C	15: 85,108,489 (GRCm39)	E75A	possibly damaging	Het
Fgf5	C	T	5: 98,409,846 (GRCm39)	R132*	probably null	Het
Folh1	T	C	7: 86,375,076 (GRCm39)		probably benign	Het
Gdf15	A	T	8: 71,082,334 (GRCm39)	H257Q	probably damaging	Het
Ghitm	T	C	14: 36,844,176 (GRCm39)	T322A	probably benign	Het
Gm5709	A	G	3: 59,526,192 (GRCm39)		noncoding transcript	Het
Hbb-y	C	T	7: 103,501,950 (GRCm39)		probably null	Het
Hmcn2	A	T	2: 31,316,210 (GRCm39)	D3771V	probably damaging	Het
Hspa12a	T	C	19: 58,787,941 (GRCm39)	D627G	probably benign	Het
Idh2	T	C	7: 79,747,662 (GRCm39)	E286G	probably damaging	Het
Idh3b	C	A	2: 130,122,899 (GRCm39)	A297S	probably benign	Het
Igsf3	A	G	3: 101,342,968 (GRCm39)	E535G	probably damaging	Het
Ilf3	T	A	9: 21,306,710 (GRCm39)	D314E	probably damaging	Het
Itgb8	A	G	12: 119,166,298 (GRCm39)	S78P	probably benign	Het
Itih5	G	A	2: 10,169,495 (GRCm39)	V31I	probably benign	Het
Kcnj2	T	C	11: 110,963,853 (GRCm39)	V415A	probably benign	Het
Kin	A	G	2: 10,090,584 (GRCm39)	Q53R	possibly damaging	Het
Krt78	A	T	15: 101,856,272 (GRCm39)	M513K	probably benign	Het
Krtap4-8	A	T	11: 99,671,312 (GRCm39)		probably benign	Het
Ltbr	T	C	6: 125,286,412 (GRCm39)		probably benign	Het
Mgat4a	G	A	1: 37,529,414 (GRCm39)	T146I	probably damaging	Het
Mrps2	G	C	2: 28,358,268 (GRCm39)	W19C	probably damaging	Het
Mthfs	T	C	9: 89,093,344 (GRCm39)	S33P	probably damaging	Het
Myh6	T	C	14: 55,196,161 (GRCm39)	D546G	probably damaging	Het
Nanos3	C	T	8: 84,902,763 (GRCm39)	R133Q	probably damaging	Het
Ndst2	T	C	14: 20,777,335 (GRCm39)	T553A	probably damaging	Het
Nlrp12	T	C	7: 3,288,664 (GRCm39)	E616G	probably damaging	Het
Nrde2	T	C	12: 100,095,545 (GRCm39)		probably benign	Het
Nup210l	G	A	3: 90,119,086 (GRCm39)	V1832I	probably benign	Het
Or1e1c	G	A	11: 73,266,402 (GRCm39)	V276I	probably benign	Het
Or4k77	A	T	2: 111,199,639 (GRCm39)	I221F	probably damaging	Het
Pcm1	A	T	8: 41,709,078 (GRCm39)	E9D	probably damaging	Het
Pear1	A	T	3: 87,661,649 (GRCm39)	D541E	possibly damaging	Het
Peg10	A	G	6: 4,756,063 (GRCm39)		probably benign	Het
Prss1	G	A	6: 41,438,166 (GRCm39)	R31Q	probably benign	Het
Ptpn13	T	C	5: 103,717,369 (GRCm39)	V1837A	probably damaging	Het
Rasgrp3	A	G	17: 75,805,456 (GRCm39)	D149G	probably damaging	Het
Reg3d	A	T	6: 78,355,466 (GRCm39)	H8Q	possibly damaging	Het
Rhox4f	A	C	X: 36,789,122 (GRCm39)	V15G	probably benign	Het
Sacs	T	A	14: 61,442,889 (GRCm39)	L1645H	probably damaging	Het
Slc16a5	A	T	11: 115,355,751 (GRCm39)	S71C	probably damaging	Het
Slc9a3	A	G	13: 74,306,847 (GRCm39)	E324G	probably damaging	Het
Smgc	T	C	15: 91,743,960 (GRCm39)	V574A	possibly damaging	Het
Stac3	C	T	10: 127,339,799 (GRCm39)		probably benign	Het
Supv3l1	A	G	10: 62,265,485 (GRCm39)	L685P	probably benign	Het
Taar2	G	A	10: 23,817,393 (GRCm39)	R311H	probably benign	Het
Tas2r125	G	T	6: 132,887,361 (GRCm39)	A250S	probably benign	Het
Tdrd6	C	T	17: 43,939,132 (GRCm39)	V639I	probably benign	Het
Thap12	T	G	7: 98,365,100 (GRCm39)	W423G	probably damaging	Het
Tmem245	T	C	4: 56,899,410 (GRCm39)	I217V	probably benign	Het
Trip12	T	A	1: 84,709,857 (GRCm39)		probably benign	Het
Tshz3	T	C	7: 36,468,317 (GRCm39)	V102A	probably benign	Het
Ubap1	T	C	4: 41,379,826 (GRCm39)	S347P	probably damaging	Het
Usp10	C	T	8: 120,679,935 (GRCm39)	Q612*	probably null	Het
Vmn2r72	T	C	7: 85,404,084 (GRCm39)	I36V	probably benign	Het
Vps37a	T	C	8: 40,980,030 (GRCm39)	I63T	possibly damaging	Het
Whrn	C	A	4: 63,350,969 (GRCm39)	R9L	possibly damaging	Het
Xrcc1	T	C	7: 24,269,642 (GRCm39)	Y401H	probably damaging	Het
Ylpm1	GCCTAAGCAGCAACCTAAG	GCCTAAG	12: 85,075,814 (GRCm39)		probably benign	Het
Zfhx3	G	A	8: 109,676,689 (GRCm39)	D2580N	possibly damaging	Het
Zfhx4	A	G	3: 5,308,685 (GRCm39)	N637S	probably damaging	Het
Zfp268	A	T	4: 145,349,195 (GRCm39)	K211*	probably null	Het
Zyg11a	A	T	4: 108,058,544 (GRCm39)		probably benign	Het

Other mutations in Col9a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00233:Col9a1	APN	1	24,224,306 (GRCm39)	missense	unknown
IGL00517:Col9a1	APN	1	24,234,615 (GRCm39)	intron	probably benign
IGL01125:Col9a1	APN	1	24,263,726 (GRCm39)	critical splice acceptor site	probably null
IGL01505:Col9a1	APN	1	24,224,205 (GRCm39)	missense	unknown
IGL01583:Col9a1	APN	1	24,224,225 (GRCm39)	missense	unknown
IGL01627:Col9a1	APN	1	24,218,689 (GRCm39)	critical splice donor site	probably null
IGL01773:Col9a1	APN	1	24,244,147 (GRCm39)	missense	probably benign	0.17
IGL02117:Col9a1	APN	1	24,276,574 (GRCm39)	nonsense	probably null
IGL02192:Col9a1	APN	1	24,261,068 (GRCm39)	missense	probably damaging	1.00
IGL02346:Col9a1	APN	1	24,262,690 (GRCm39)	missense	probably damaging	0.96
IGL02383:Col9a1	APN	1	24,224,339 (GRCm39)	missense	unknown
IGL02453:Col9a1	APN	1	24,218,438 (GRCm39)	missense	unknown
IGL02553:Col9a1	APN	1	24,261,018 (GRCm39)	splice site	probably benign
IGL03412:Col9a1	APN	1	24,249,508 (GRCm39)	critical splice donor site	probably null
IGL03493:Col9a1	APN	1	24,260,651 (GRCm39)	splice site	probably benign
ANU74:Col9a1	UTSW	1	24,224,409 (GRCm39)	missense	unknown
R0076:Col9a1	UTSW	1	24,276,578 (GRCm39)	critical splice donor site	probably null
R0076:Col9a1	UTSW	1	24,276,578 (GRCm39)	critical splice donor site	probably null
R0356:Col9a1	UTSW	1	24,224,328 (GRCm39)	nonsense	probably null
R0562:Col9a1	UTSW	1	24,218,360 (GRCm39)	splice site	probably null
R0584:Col9a1	UTSW	1	24,263,571 (GRCm39)	splice site	probably benign
R0708:Col9a1	UTSW	1	24,276,342 (GRCm39)	missense	possibly damaging	0.92
R1342:Col9a1	UTSW	1	24,262,701 (GRCm39)	critical splice donor site	probably null
R1445:Col9a1	UTSW	1	24,276,579 (GRCm39)	critical splice donor site	probably null
R1791:Col9a1	UTSW	1	24,224,386 (GRCm39)	missense	unknown
R1938:Col9a1	UTSW	1	24,261,554 (GRCm39)	missense	probably damaging	1.00
R2214:Col9a1	UTSW	1	24,247,283 (GRCm39)	missense	probably damaging	1.00
R2240:Col9a1	UTSW	1	24,218,582 (GRCm39)	missense	unknown
R3757:Col9a1	UTSW	1	24,271,312 (GRCm39)	critical splice donor site	probably null
R3891:Col9a1	UTSW	1	24,224,517 (GRCm39)	critical splice donor site	probably null
R4249:Col9a1	UTSW	1	24,283,462 (GRCm39)	missense	probably damaging	1.00
R4690:Col9a1	UTSW	1	24,263,787 (GRCm39)	splice site	probably null
R4918:Col9a1	UTSW	1	24,276,339 (GRCm39)	missense	possibly damaging	0.74
R4988:Col9a1	UTSW	1	24,224,273 (GRCm39)	missense	unknown
R5144:Col9a1	UTSW	1	24,278,434 (GRCm39)	missense	probably benign	0.08
R5327:Col9a1	UTSW	1	24,234,620 (GRCm39)	critical splice donor site	probably null
R5511:Col9a1	UTSW	1	24,218,619 (GRCm39)	missense	unknown
R5519:Col9a1	UTSW	1	24,269,335 (GRCm39)	splice site	probably null
R5564:Col9a1	UTSW	1	24,234,436 (GRCm39)	start gained	probably benign
R6076:Col9a1	UTSW	1	24,234,457 (GRCm39)	start gained	probably benign
R6478:Col9a1	UTSW	1	24,224,486 (GRCm39)	missense	unknown
R6886:Col9a1	UTSW	1	24,224,426 (GRCm39)	missense	unknown
R7177:Col9a1	UTSW	1	24,234,498 (GRCm39)	missense	unknown
R7259:Col9a1	UTSW	1	24,224,424 (GRCm39)	missense	unknown
R7268:Col9a1	UTSW	1	24,246,479 (GRCm39)	missense	possibly damaging	0.89
R7347:Col9a1	UTSW	1	24,218,484 (GRCm39)	splice site	probably null
R7644:Col9a1	UTSW	1	24,224,243 (GRCm39)	missense	unknown
R7860:Col9a1	UTSW	1	24,276,261 (GRCm39)	missense	probably damaging	1.00
R8267:Col9a1	UTSW	1	24,224,267 (GRCm39)	missense	unknown
R8296:Col9a1	UTSW	1	24,217,380 (GRCm39)	missense	unknown
R8737:Col9a1	UTSW	1	24,224,127 (GRCm39)	missense	unknown
R8773:Col9a1	UTSW	1	24,224,208 (GRCm39)	missense	unknown
R8795:Col9a1	UTSW	1	24,233,812 (GRCm39)	missense	unknown
R8878:Col9a1	UTSW	1	24,236,048 (GRCm39)	critical splice donor site	probably null
R8956:Col9a1	UTSW	1	24,276,300 (GRCm39)	missense	probably damaging	1.00
R8978:Col9a1	UTSW	1	24,278,396 (GRCm39)	missense	probably damaging	1.00
R9096:Col9a1	UTSW	1	24,224,207 (GRCm39)	missense	unknown
R9097:Col9a1	UTSW	1	24,224,207 (GRCm39)	missense	unknown
R9205:Col9a1	UTSW	1	24,224,175 (GRCm39)	missense	unknown
R9534:Col9a1	UTSW	1	24,224,250 (GRCm39)	missense	unknown
Z1176:Col9a1	UTSW	1	24,253,669 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTTAACACGCTTAACAAGGCACGG -3'
(R):5'- AGTCTCATCAGCCATTTTCCACAGC -3'

Sequencing Primer
(F):5'- GGGAAAGCCTCACGCTAC -3'
(R):5'- AAAGGATTTTGCTTTCTGATTTCTCC -3'

Posted On

2013-04-11