Mutagenetix > Incidental Mutation

Incidental Mutation 'R7644:Col9a1'

590385

Institutional Source

Beutler Lab

Gene Symbol

Col9a1

Ensembl Gene

ENSMUSG00000026147

Gene Name

collagen, type IX, alpha 1

Synonyms

Col9a-1

MMRRC Submission

045723-MU

Accession Numbers

Essential gene?

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

Stock #

R7644 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

24216691-24291765 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 24224243 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Phenylalanine at position 142 (V142F)

Ref Sequence

ENSEMBL: ENSMUSP00000051579 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

unknown
Transcript: ENSMUST00000054588
AA Change: V142F

SMART Domains

Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147
AA Change: V142F

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

100% (86/86)

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: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700001O22Rik	C	T	2: 30,687,966 (GRCm39)	R209Q	possibly damaging	Het
Abl2	A	G	1: 156,443,563 (GRCm39)	D24G	probably benign	Het
Adar	C	T	3: 89,652,826 (GRCm39)	A754V	probably benign	Het
Adcy8	C	T	15: 64,571,218 (GRCm39)	V1172I	possibly damaging	Het
Adgrl2	C	T	3: 148,544,789 (GRCm39)	V769M	probably damaging	Het
Akna	T	A	4: 63,313,634 (GRCm39)	Q163L	possibly damaging	Het
Alox15	C	T	11: 70,236,368 (GRCm39)	A511T	probably null	Het
Ano8	C	T	8: 71,937,474 (GRCm39)	G90D	probably damaging	Het
Aqp5	G	A	15: 99,492,107 (GRCm39)	R235H	probably damaging	Het
B3galt4	A	T	17: 34,169,419 (GRCm39)	V273E	probably damaging	Het
Ccdc125	C	T	13: 100,814,884 (GRCm39)		probably null	Het
Ccdc90b	A	G	7: 92,216,868 (GRCm39)	R47G	possibly damaging	Het
Celsr2	G	T	3: 108,320,806 (GRCm39)	L669I	probably damaging	Het
Clasp1	T	G	1: 118,440,480 (GRCm39)		probably null	Het
Clec4a2	C	T	6: 123,101,974 (GRCm39)	P43L	probably benign	Het
Cntn1	T	C	15: 92,207,890 (GRCm39)	I827T	probably benign	Het
Cplane1	T	A	15: 8,252,611 (GRCm39)	D1944E	probably benign	Het
Cts7	G	T	13: 61,504,782 (GRCm39)	Y23*	probably null	Het
Dcdc2a	T	A	13: 25,291,674 (GRCm39)	Y220N	probably damaging	Het
Dennd2b	A	T	7: 109,156,000 (GRCm39)	L250*	probably null	Het
Dmxl1	T	G	18: 50,026,619 (GRCm39)	V1909G	probably benign	Het
Ehd2	G	A	7: 15,691,474 (GRCm39)	P286L	possibly damaging	Het
Elf3	G	T	1: 135,184,244 (GRCm39)	A208E	possibly damaging	Het
Eml5	A	G	12: 98,822,203 (GRCm39)	I775T	probably benign	Het
Ephb1	T	C	9: 101,813,393 (GRCm39)	T791A	probably damaging	Het
Fanci	C	A	7: 79,094,219 (GRCm39)	S1105*	probably null	Het
Fastkd1	T	A	2: 69,527,184 (GRCm39)		probably null	Het
Fat4	A	G	3: 39,064,390 (GRCm39)	E4782G	possibly damaging	Het
Fnta	T	C	8: 26,503,516 (GRCm39)	I90V	probably damaging	Het
Fosl1	C	T	19: 5,500,332 (GRCm39)	R84*	probably null	Het
Gdf2	T	C	14: 33,666,847 (GRCm39)	F190L	probably benign	Het
Gzmn	T	A	14: 56,404,776 (GRCm39)	Q88L	probably damaging	Het
Hat1	T	A	2: 71,240,525 (GRCm39)	L73Q	probably damaging	Het
Hdhd2	G	A	18: 77,031,871 (GRCm39)	G109E	possibly damaging	Het
Il22ra1	A	G	4: 135,460,346 (GRCm39)	N34S	probably damaging	Het
Ino80d	T	C	1: 63,097,930 (GRCm39)	T760A	probably benign	Het
Itga7	A	G	10: 128,789,370 (GRCm39)	D971G	probably benign	Het
Kdm6b	T	C	11: 69,291,032 (GRCm39)	N1574S	unknown	Het
Kel	T	C	6: 41,667,742 (GRCm39)	E400G	probably benign	Het
Kif22	G	A	7: 126,632,134 (GRCm39)	T350I	probably damaging	Het
Kif26b	A	G	1: 178,506,839 (GRCm39)	N305S	probably benign	Het
Klk12	A	C	7: 43,419,134 (GRCm39)	Q33P	probably damaging	Het
Klk1b24	G	A	7: 43,841,304 (GRCm39)		probably null	Het
Krtap31-1	T	A	11: 99,799,048 (GRCm39)	C84S	possibly damaging	Het
Ky	T	A	9: 102,414,972 (GRCm39)	S295T	probably benign	Het
Lpin3	T	A	2: 160,738,690 (GRCm39)	M214K	probably benign	Het
Mak	T	A	13: 41,183,586 (GRCm39)	N565Y	probably benign	Het
Mphosph6	T	C	8: 118,528,623 (GRCm39)	T7A	probably benign	Het
Muc6	G	C	7: 141,217,659 (GRCm39)	P2338R	probably damaging	Het
Myh11	T	C	16: 14,039,688 (GRCm39)	T814A		Het
Nmbr	T	C	10: 14,636,433 (GRCm39)	L134P	probably damaging	Het
Nup107	C	T	10: 117,606,375 (GRCm39)	V456M	probably damaging	Het
Or56b1b	A	G	7: 108,164,649 (GRCm39)	S118P	possibly damaging	Het
Or8g22	C	A	9: 38,958,638 (GRCm39)	D26Y	probably damaging	Het
Pink1	A	T	4: 138,044,683 (GRCm39)	H351Q	probably damaging	Het
Piwil4	A	T	9: 14,645,711 (GRCm39)		probably null	Het
Pkd1l1	C	A	11: 8,825,758 (GRCm39)	V1498F		Het
Polb	A	G	8: 23,130,443 (GRCm39)	I161T	probably benign	Het
Polg	A	T	7: 79,101,416 (GRCm39)	L1097Q	probably damaging	Het
Prelp	T	C	1: 133,842,356 (GRCm39)	N263S	probably benign	Het
Pten	T	C	19: 32,789,234 (GRCm39)	C211R	probably damaging	Het
Ptprc	G	A	1: 137,995,645 (GRCm39)	A1012V	probably benign	Het
Ptprr	T	A	10: 115,884,133 (GRCm39)	H63Q	probably benign	Het
Rapsn	A	T	2: 90,872,299 (GRCm39)	H211L	possibly damaging	Het
Reln	T	C	5: 22,183,929 (GRCm39)	N1690S	probably benign	Het
Rpap2	A	G	5: 107,768,167 (GRCm39)	E335G	probably benign	Het
Rspry1	T	A	8: 95,385,396 (GRCm39)	S567T	probably benign	Het
Sf3b1	G	A	1: 55,036,302 (GRCm39)	R924*	probably null	Het
Sftpb	G	A	6: 72,286,818 (GRCm39)	E241K	probably benign	Het
Smarca4	G	T	9: 21,566,950 (GRCm39)	A677S	probably benign	Het
Srrm2	G	A	17: 24,038,294 (GRCm39)	R1646Q	unknown	Het
Tex15	T	A	8: 34,064,445 (GRCm39)	C1292S	probably benign	Het
Tmem140	A	G	6: 34,849,708 (GRCm39)	I75V	probably benign	Het
Trhr2	T	A	8: 123,084,061 (GRCm39)	Q313L	possibly damaging	Het
Trim35	A	G	14: 66,534,546 (GRCm39)	T10A	unknown	Het
Ttn	T	C	2: 76,750,124 (GRCm39)	I3642V	probably benign	Het
Ugt1a2	T	C	1: 88,128,507 (GRCm39)	L50P	probably damaging	Het
Unc13a	C	A	8: 72,087,182 (GRCm39)	V1522L	probably benign	Het
Usp33	A	G	3: 152,063,589 (GRCm39)	D21G	possibly damaging	Het
Vmn1r90	G	A	7: 14,295,616 (GRCm39)	Q161*	probably null	Het
Vmn2r117	A	T	17: 23,696,265 (GRCm39)	W381R	probably damaging	Het
Vmn2r16	G	C	5: 109,487,837 (GRCm39)	A237P	probably damaging	Het
Vmn2r74	A	G	7: 85,606,746 (GRCm39)	V200A	probably benign	Het
Yjefn3	C	T	8: 70,340,544 (GRCm39)	V227M	probably damaging	Het
Zfp652	T	C	11: 95,640,914 (GRCm39)	F280L	probably damaging	Het
Zfp748	G	A	13: 67,689,568 (GRCm39)	T564I	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
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
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'- ACACTGTAGCCTTTCCGCAG -3'
(R):5'- ATAGGTAAAGATTCGATCCTGATGC -3'

Sequencing Primer
(F):5'- AGCACACACACAGAAAAATGG -3'
(R):5'- CGATCCTGATGCAGTCAATAAAAAG -3'

Posted On

2019-10-24