Mutagenetix > Incidental Mutation

Incidental Mutation 'R4690:Col9a1'

386369

Institutional Source

Beutler Lab

Gene Symbol

Col9a1

Ensembl Gene

ENSMUSG00000026147

Gene Name

collagen, type IX, alpha 1

Synonyms

Col9a-1

MMRRC Submission

041941-MU

Accession Numbers

Essential gene?

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

Stock #

R4690 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

24216691-24291765 bp(+) (GRCm39)

Type of Mutation

splice site (6 bp from exon)

DNA Base Change (assembly)

T to C at 24263787 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000085687 (fasta)

Gene Model

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000147902

Meta Mutation Damage Score

0.9755

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.5%

Validation Efficiency

98% (89/91)

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: 85 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca9	A	G	11: 110,039,706 (GRCm39)	F436L	probably damaging	Het
Adam28	G	T	14: 68,879,497 (GRCm39)	Q184K	probably benign	Het
Adh6a	A	G	3: 138,031,932 (GRCm39)	T275A	possibly damaging	Het
Agap2	A	G	10: 126,927,244 (GRCm39)	D1082G	possibly damaging	Het
Alox5	A	T	6: 116,400,150 (GRCm39)	V263E	probably damaging	Het
Arhgef16	C	T	4: 154,372,420 (GRCm39)		probably null	Het
Bspry	G	A	4: 62,404,762 (GRCm39)	R186Q	probably damaging	Het
Ccdc188	T	A	16: 18,036,159 (GRCm39)	H111Q	probably damaging	Het
Cd40	T	C	2: 164,911,615 (GRCm39)	F209S	possibly damaging	Het
Cfap43	C	A	19: 47,736,298 (GRCm39)	V1398L	probably benign	Het
Cln3	A	T	7: 126,174,565 (GRCm39)	I286N	possibly damaging	Het
Cpne9	A	G	6: 113,279,016 (GRCm39)	E470G	probably damaging	Het
Cul5	A	T	9: 53,534,171 (GRCm39)	W654R	probably damaging	Het
Cyp2a22	T	A	7: 26,638,634 (GRCm39)	K51*	probably null	Het
Dcaf10	G	A	4: 45,372,769 (GRCm39)	R394Q	possibly damaging	Het
Dot1l	C	A	10: 80,622,016 (GRCm39)	S556*	probably null	Het
Eif3d	A	T	15: 77,851,516 (GRCm39)	M98K	probably benign	Het
Fiz1	A	G	7: 5,012,167 (GRCm39)	V117A	probably benign	Het
Fryl	A	G	5: 73,257,636 (GRCm39)	V722A	probably benign	Het
Ftdc1	G	A	16: 58,434,333 (GRCm39)	T128I	probably benign	Het
Gm3095	G	T	14: 3,964,471 (GRCm38)	R63I	probably benign	Het
Gm7133	A	T	1: 97,197,224 (GRCm39)		noncoding transcript	Het
Hoxb8	A	T	11: 96,175,286 (GRCm39)	D241V	probably benign	Het
Hrnr	A	G	3: 93,230,959 (GRCm39)	Q399R	unknown	Het
Itpk1	A	T	12: 102,572,434 (GRCm39)	V93D	probably damaging	Het
Kars1	C	T	8: 112,729,216 (GRCm39)	A164T	probably benign	Het
Kcnq4	A	T	4: 120,574,208 (GRCm39)	I150N	probably damaging	Het
Kcnrg	A	T	14: 61,849,176 (GRCm39)	L212F	probably damaging	Het
Kif5b	A	T	18: 6,216,759 (GRCm39)	D521E	probably benign	Het
Klf11	C	T	12: 24,705,071 (GRCm39)	T158M	probably damaging	Het
Klhl6	T	C	16: 19,776,034 (GRCm39)	I175V	probably benign	Het
Lsm1	A	G	8: 26,283,708 (GRCm39)	N40S	probably damaging	Het
Map1b	T	C	13: 99,567,576 (GRCm39)	E1715G	unknown	Het
Mecom	C	A	3: 30,292,459 (GRCm39)	A4S	probably benign	Het
Muc5b	G	A	7: 141,396,031 (GRCm39)	V96M	unknown	Het
Mug2	A	T	6: 122,013,255 (GRCm39)	I341L	probably benign	Het
Mxra7	A	T	11: 116,707,078 (GRCm39)		probably null	Het
Myo5a	T	C	9: 75,061,105 (GRCm39)	L537P	probably damaging	Het
Myo5b	A	T	18: 74,855,533 (GRCm39)	N1241Y	probably damaging	Het
Naa16	T	C	14: 79,582,497 (GRCm39)	R531G	probably damaging	Het
Neb	T	A	2: 52,134,087 (GRCm39)	M3299L	probably benign	Het
Nlrp4b	T	A	7: 10,453,130 (GRCm39)	Y76N	probably benign	Het
Nmral1	T	C	16: 4,534,205 (GRCm39)	T79A	probably damaging	Het
Noct	C	T	3: 51,155,300 (GRCm39)	Q23*	probably null	Het
Nrxn1	A	T	17: 90,344,509 (GRCm39)	V438D	probably damaging	Het
Or5b109	A	C	19: 13,212,132 (GRCm39)	N173H	possibly damaging	Het
Or5m9	T	A	2: 85,877,242 (GRCm39)	C139S	probably damaging	Het
Oxct2a	T	C	4: 123,216,836 (GRCm39)	T182A	probably benign	Het
Pank2	T	C	2: 131,115,945 (GRCm39)	I121T	probably damaging	Het
Pcdh1	T	A	18: 38,336,528 (GRCm39)	T36S	probably benign	Het
Pfdn1	A	T	18: 36,584,133 (GRCm39)	M67K	possibly damaging	Het
Plec	T	C	15: 76,058,456 (GRCm39)	E3849G	probably damaging	Het
Polr3a	A	T	14: 24,514,349 (GRCm39)	S817T	possibly damaging	Het
Pomgnt1	T	A	4: 116,012,707 (GRCm39)	D401E	probably damaging	Het
Ppp1r13b	T	A	12: 111,798,992 (GRCm39)	D891V	probably damaging	Het
Prr14l	A	G	5: 33,001,500 (GRCm39)		probably benign	Het
Ptk2b	A	G	14: 66,410,749 (GRCm39)		probably null	Het
Rab13	G	C	3: 90,128,330 (GRCm39)		probably null	Het
Rexo1	C	T	10: 80,382,255 (GRCm39)	A751T	probably benign	Het
Rfx1	T	C	8: 84,809,374 (GRCm39)	V233A	possibly damaging	Het
Rnf149	C	T	1: 39,616,295 (GRCm39)		probably benign	Het
Rrm1	A	G	7: 102,097,086 (GRCm39)	D122G	probably benign	Het
Serpina1b	A	G	12: 103,698,639 (GRCm39)	F70S	probably damaging	Het
Serpinb13	C	T	1: 106,910,574 (GRCm39)	S66L	probably damaging	Het
Sh3rf3	T	C	10: 58,649,526 (GRCm39)	S44P	possibly damaging	Het
Shroom1	A	G	11: 53,356,549 (GRCm39)	T471A	possibly damaging	Het
Slc6a1	A	G	6: 114,279,792 (GRCm39)	Y152C	probably damaging	Het
Spata31f3	T	A	4: 42,873,032 (GRCm39)		probably null	Het
Spata6	A	T	4: 111,632,023 (GRCm39)	T145S	probably damaging	Het
Srcap	G	A	7: 127,137,186 (GRCm39)	G956D	probably damaging	Het
Ssh2	A	T	11: 77,346,031 (GRCm39)	I1339F	possibly damaging	Het
Tardbp	A	T	4: 148,697,078 (GRCm39)	*99K	probably null	Het
Tbc1d22a	A	G	15: 86,196,037 (GRCm39)	Y336C	probably damaging	Het
Tmcc3	G	A	10: 94,381,419 (GRCm39)		probably benign	Het
Tmem178b	T	G	6: 40,222,547 (GRCm39)	D87E	probably benign	Het
Tmem184a	A	C	5: 139,791,377 (GRCm39)	S380A	probably benign	Het
Tnfaip2	A	G	12: 111,411,682 (GRCm39)	K84R	possibly damaging	Het
Tpgs1	A	G	10: 79,511,235 (GRCm39)	T126A	probably benign	Het
Traf3ip1	A	G	1: 91,447,834 (GRCm39)	E437G	possibly damaging	Het
Trpc4ap	C	T	2: 155,477,053 (GRCm39)	C755Y	probably damaging	Het
Tsfm	A	G	10: 126,866,547 (GRCm39)		probably benign	Het
Tulp1	A	C	17: 28,570,811 (GRCm39)		probably benign	Het
Vmn1r23	A	T	6: 57,903,010 (GRCm39)	M256K	probably benign	Het
Zdhhc8	T	C	16: 18,044,605 (GRCm39)	D305G	probably damaging	Het
Zfp326	G	A	5: 106,054,942 (GRCm39)	R282H	probably damaging	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
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
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'- TTAGGGTAACACGGGTGCTC -3'
(R):5'- GAGAATAAAAGCCCCTTTATGCTTC -3'

Sequencing Primer
(F):5'- CAGGAAAGCCCGGTCAGTTG -3'
(R):5'- ACACATCATTTTGGTTCCAGTTTTGG -3'

Posted On

2016-05-20