Mutagenetix > Incidental Mutation

Incidental Mutation 'R1938:Col9a1'

213611

Institutional Source

Beutler Lab

Gene Symbol

Col9a1

Ensembl Gene

ENSMUSG00000026147

Gene Name

collagen, type IX, alpha 1

Synonyms

Col9a-1

MMRRC Submission

039956-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.092) question?

Stock #

R1938 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

24216691-24291765 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 24261554 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Serine at position 573 (P573S)

Ref Sequence

ENSEMBL: ENSMUSP00000051579 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000054588
AA Change: P573S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: P573S

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 damaging
Transcript: ENSMUST00000088349
AA Change: P332S

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147
AA Change: P332S

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

Coding Region Coverage

1x: 97.5%
3x: 96.9%
10x: 95.4%
20x: 92.8%

Validation Efficiency

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: 133 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc8	T	C	7: 45,824,795 (GRCm39)	K134R	possibly damaging	Het
Adamts17	T	C	7: 66,774,820 (GRCm39)	S980P	probably damaging	Het
Adap2	T	A	11: 80,061,508 (GRCm39)	I221K	probably damaging	Het
Adgrv1	C	T	13: 81,539,876 (GRCm39)	R5681Q	probably damaging	Het
Adipor1	T	A	1: 134,350,841 (GRCm39)	L30Q	probably benign	Het
Agpat5	A	G	8: 18,928,181 (GRCm39)	T249A	probably benign	Het
Agxt2	G	T	15: 10,392,021 (GRCm39)	G329V	probably damaging	Het
Ankrd28	A	G	14: 31,427,233 (GRCm39)	V801A	possibly damaging	Het
Ap1g2	A	G	14: 55,337,229 (GRCm39)	V702A	possibly damaging	Het
Arid3a	A	G	10: 79,786,540 (GRCm39)	Q429R	probably damaging	Het
Arsb	T	A	13: 93,998,658 (GRCm39)	L322Q	probably damaging	Het
Ash1l	A	G	3: 88,891,729 (GRCm39)	T1203A	probably damaging	Het
Atad2	T	A	15: 57,960,101 (GRCm39)	N1308Y	possibly damaging	Het
Atp10b	A	T	11: 43,121,245 (GRCm39)	R969S	probably benign	Het
Bmp10	T	C	6: 87,410,702 (GRCm39)	I165T	possibly damaging	Het
Ccdc121rt2	C	A	5: 112,597,667 (GRCm39)	C71*	probably null	Het
Ccne1	A	G	7: 37,805,702 (GRCm39)		probably null	Het
Cenpe	A	G	3: 134,953,240 (GRCm39)	N1565D	probably damaging	Het
Chd1	A	T	17: 15,982,748 (GRCm39)	E1404D	probably benign	Het
Chd7	G	A	4: 8,847,200 (GRCm39)	E1648K	probably damaging	Het
Chodl	T	C	16: 78,738,314 (GRCm39)	I94T	possibly damaging	Het
Chsy3	T	C	18: 59,542,584 (GRCm39)	F574S	probably damaging	Het
Clpb	A	T	7: 101,412,863 (GRCm39)	I317F	probably damaging	Het
Cnga3	T	A	1: 37,300,954 (GRCm39)	V558D	possibly damaging	Het
Crat	A	T	2: 30,303,073 (GRCm39)	D71E	probably benign	Het
Cspg4	A	G	9: 56,794,385 (GRCm39)	T707A	probably benign	Het
Ctsr	T	A	13: 61,310,259 (GRCm39)	R132S	probably benign	Het
Ctu2	T	C	8: 123,206,024 (GRCm39)	L255P	probably damaging	Het
Cyp2c69	T	C	19: 39,837,810 (GRCm39)	Y424C	probably damaging	Het
Ddx27	A	T	2: 166,876,029 (GRCm39)	K726N	probably damaging	Het
Dennd4a	A	G	9: 64,749,772 (GRCm39)	Q121R	probably damaging	Het
Dis3	A	G	14: 99,335,026 (GRCm39)	F192S	probably benign	Het
Ect2l	C	T	10: 18,020,383 (GRCm39)	S487N	probably benign	Het
Eml1	T	A	12: 108,487,655 (GRCm39)	F524L	possibly damaging	Het
Espl1	T	C	15: 102,213,477 (GRCm39)	I601T	probably benign	Het
Fbxo40	C	A	16: 36,789,713 (GRCm39)	V466L	probably damaging	Het
Frmpd1	C	T	4: 45,283,711 (GRCm39)	T844M	probably damaging	Het
Frs2	T	A	10: 116,917,011 (GRCm39)		probably benign	Het
Fuom	G	T	7: 139,679,521 (GRCm39)	T133K	probably benign	Het
Garnl3	T	A	2: 32,895,212 (GRCm39)	H619L	probably damaging	Het
Gm4861	G	T	3: 137,257,876 (GRCm39)	N36K	unknown	Het
Gps2	G	T	11: 69,806,195 (GRCm39)	M153I	probably benign	Het
Gtf2ird1	A	G	5: 134,444,099 (GRCm39)	V52A	probably damaging	Het
Gtpbp8	A	T	16: 44,565,785 (GRCm39)	D137E	probably benign	Het
Haus4	A	G	14: 54,781,733 (GRCm39)	C213R	probably damaging	Het
Hdc	T	A	2: 126,448,317 (GRCm39)	H142L	possibly damaging	Het
Hephl1	T	C	9: 14,965,283 (GRCm39)	D1069G	possibly damaging	Het
Herc6	T	A	6: 57,602,926 (GRCm39)	V535D	probably damaging	Het
Hipk3	A	T	2: 104,260,533 (GRCm39)	H1082Q	possibly damaging	Het
Hps5	A	T	7: 46,422,691 (GRCm39)	V513D	probably damaging	Het
Ifna13	T	A	4: 88,562,412 (GRCm39)	I71F	probably damaging	Het
Il1rl2	T	C	1: 40,402,484 (GRCm39)	I426T	probably damaging	Het
Irf5	A	T	6: 29,536,738 (GRCm39)	D483V	probably benign	Het
Jakmip3	A	G	7: 138,621,867 (GRCm39)	R256G	probably damaging	Het
Jazf1	T	C	6: 52,754,600 (GRCm39)	I159V	probably damaging	Het
Kmo	A	G	1: 175,479,154 (GRCm39)	D230G	possibly damaging	Het
Lrrc74b	A	G	16: 17,371,058 (GRCm39)	V213A	probably benign	Het
LTO1	A	G	7: 144,470,205 (GRCm39)	S45G	probably damaging	Het
Ly6g5b	T	C	17: 35,333,704 (GRCm39)	D36G	possibly damaging	Het
Mab21l4	T	C	1: 93,079,730 (GRCm39)	*453W	probably null	Het
Macc1	T	G	12: 119,409,466 (GRCm39)	L78R	probably damaging	Het
Mettl4	A	T	17: 95,055,285 (GRCm39)	D51E	possibly damaging	Het
Mfap1a	G	A	2: 121,332,835 (GRCm39)	L199F	possibly damaging	Het
Mmp17	G	T	5: 129,679,190 (GRCm39)	R363L	probably damaging	Het
Mrc1	G	A	2: 14,324,052 (GRCm39)	A1130T	possibly damaging	Het
Mrpl15	C	T	1: 4,847,805 (GRCm39)	A165T	probably damaging	Het
Mrpl45	G	A	11: 97,206,770 (GRCm39)		probably null	Het
Ms4a3	C	T	19: 11,613,204 (GRCm39)	A85T	possibly damaging	Het
Mttp	A	T	3: 137,830,882 (GRCm39)	D77E	probably benign	Het
Muc6	A	G	7: 141,217,011 (GRCm39)	L2489P	probably damaging	Het
Myl3	G	A	9: 110,595,802 (GRCm39)	E100K	probably damaging	Het
Nbea	T	A	3: 55,992,743 (GRCm39)	N288Y	probably damaging	Het
Ncoa7	A	G	10: 30,574,166 (GRCm39)	V181A	probably benign	Het
Oat	C	T	7: 132,159,934 (GRCm39)	V429M	probably benign	Het
Or2ak6	A	T	11: 58,593,449 (GRCm39)	*307C	probably null	Het
Or4x6	T	G	2: 89,949,427 (GRCm39)	I172L	probably damaging	Het
Or5d36	A	T	2: 87,901,300 (GRCm39)	L142Q	probably damaging	Het
Or5p80	T	C	7: 108,230,045 (GRCm39)	I282T	probably benign	Het
Or5w19	G	A	2: 87,698,805 (GRCm39)	V157I	probably benign	Het
Or6b13	A	G	7: 139,782,144 (GRCm39)	F180L	probably benign	Het
Or6c69b	T	A	10: 129,626,759 (GRCm39)	K233M	probably damaging	Het
Or8b55	A	G	9: 38,727,146 (GRCm39)	T116A	probably benign	Het
Or8s16	T	A	15: 98,211,261 (GRCm39)	M57L	probably damaging	Het
Otof	A	G	5: 30,533,713 (GRCm39)	S1464P	probably benign	Het
Otogl	A	T	10: 107,613,436 (GRCm39)	Y2010N	probably damaging	Het
Pgap3	C	T	11: 98,291,040 (GRCm39)		probably null	Het
Pgbd5	T	A	8: 125,100,988 (GRCm39)	K332*	probably null	Het
Pgs1	C	T	11: 117,896,553 (GRCm39)	P410L	probably damaging	Het
Pkhd1l1	G	A	15: 44,363,434 (GRCm39)	S618N	probably benign	Het
Plcb1	A	T	2: 135,228,222 (GRCm39)	D1073V	probably damaging	Het
Pola2	T	A	19: 6,001,208 (GRCm39)	T309S	probably benign	Het
Polg2	T	A	11: 106,669,787 (GRCm39)	H161L	probably damaging	Het
Postn	T	A	3: 54,285,033 (GRCm39)		probably null	Het
Ppt1	G	T	4: 122,739,784 (GRCm39)	C128F	probably damaging	Het
Ptpn12	G	A	5: 21,198,261 (GRCm39)	P678S	probably damaging	Het
Rcan3	A	T	4: 135,139,812 (GRCm39)		probably null	Het
Rgs22	T	C	15: 36,101,950 (GRCm39)	N216S	probably benign	Het
Rgs7bp	T	A	13: 105,088,090 (GRCm39)	D228V	probably damaging	Het
Rhobtb2	A	T	14: 70,034,062 (GRCm39)	S388T	probably benign	Het
Rnps1	C	T	17: 24,639,364 (GRCm39)	R138C	unknown	Het
Rpl38	T	C	11: 114,562,602 (GRCm39)	V36A	probably benign	Het
Rps7	G	T	12: 28,681,752 (GRCm39)	H126Q	possibly damaging	Het
Sec24b	G	T	3: 129,785,010 (GRCm39)	Q999K	possibly damaging	Het
Slc19a3	A	G	1: 82,997,089 (GRCm39)	V373A	possibly damaging	Het
Spats2l	T	A	1: 57,924,941 (GRCm39)	V113E	probably benign	Het
Ss18l1	A	T	2: 179,705,138 (GRCm39)	T377S	unknown	Het
Surf1	A	G	2: 26,805,982 (GRCm39)	F38L	probably benign	Het
Ticrr	G	A	7: 79,325,142 (GRCm39)	R556H	probably damaging	Het
Tmem184b	A	G	15: 79,250,014 (GRCm39)	S254P	probably damaging	Het
Tnfrsf4	G	T	4: 156,100,692 (GRCm39)	R237L	possibly damaging	Het
Tnk2	C	A	16: 32,482,560 (GRCm39)		probably benign	Het
Tnks	A	T	8: 35,305,684 (GRCm39)	D1191E	probably damaging	Het
Tnr	C	A	1: 159,722,607 (GRCm39)	Y1017*	probably null	Het
Tomm34	A	G	2: 163,902,926 (GRCm39)	I128T	probably benign	Het
Trim2	G	A	3: 84,085,099 (GRCm39)	S540F	possibly damaging	Het
Trio	A	T	15: 27,732,977 (GRCm39)	I2968N	probably damaging	Het
Ttc24	T	C	3: 87,982,181 (GRCm39)	E17G	probably benign	Het
Ttc41	A	G	10: 86,612,078 (GRCm39)	H1117R	probably benign	Het
Ttn	A	T	2: 76,565,752 (GRCm39)	V28200D	probably damaging	Het
Ttn	A	T	2: 76,592,730 (GRCm39)	S20801T	possibly damaging	Het
Ube3d	C	T	9: 86,330,840 (GRCm39)	C114Y	probably damaging	Het
Ugt2b37	A	C	5: 87,388,716 (GRCm39)	L499R	probably damaging	Het
Vmn1r81	T	C	7: 11,994,589 (GRCm39)	I6M	possibly damaging	Het
Vmn2r97	A	T	17: 19,149,593 (GRCm39)	Y327F	probably benign	Het
Vps13b	T	C	15: 35,709,653 (GRCm39)	S1867P	probably damaging	Het
Wdr11	T	C	7: 129,208,331 (GRCm39)	V362A	probably benign	Het
Zan	T	A	5: 137,387,201 (GRCm39)	M4951L	unknown	Het
Zcwpw1	T	A	5: 137,809,884 (GRCm39)	L337Q	probably damaging	Het
Zfp2	A	T	11: 50,790,809 (GRCm39)	D411E	possibly damaging	Het
Zfp628	C	T	7: 4,923,767 (GRCm39)	T663I	probably benign	Het
Zfpm1	T	A	8: 123,061,663 (GRCm39)		probably null	Het
Zfyve19	T	C	2: 119,041,693 (GRCm39)	S87P	probably benign	Het
Zswim9	T	A	7: 12,994,141 (GRCm39)	K672*	probably null	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
R0090:Col9a1	UTSW	1	24,262,643 (GRCm39)	splice 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
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'- CACTGATGAGTGTAGGCTGAAG -3'
(R):5'- TGACCAGCTAGCTAACCCTAAG -3'

Sequencing Primer
(F):5'- TGAGTGTAGGCTGAAGGAAATTC -3'
(R):5'- CCTAAGGGGGAAACAAAATT -3'

Posted On

2014-07-14