Mutagenetix > Incidental Mutation

Incidental Mutation 'R0973:Col9a2'

236718

Institutional Source

Beutler Lab

Gene Symbol

Col9a2

Ensembl Gene

ENSMUSG00000028626

Gene Name

collagen, type IX, alpha 2

Synonyms

Col9a-2

MMRRC Submission

039102-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0973 (G1)

Quality Score

182

Status

Validated

Chromosome

Chromosomal Location

120896763-120912522 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to A at 120896985 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000030372 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030372]

AlphaFold

no structure available at present

Predicted Effect

probably null
Transcript: ENSMUST00000030372

SMART Domains

Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
Pfam:Collagen	24	82	7.3e-12	PFAM
Pfam:Collagen	59	115	2.4e-10	PFAM
Pfam:Collagen	113	170	2e-8	PFAM
Pfam:Collagen	176	236	8.9e-11	PFAM
low complexity region	258	277	N/A	INTRINSIC
low complexity region	288	315	N/A	INTRINSIC
Pfam:Collagen	357	435	4.4e-8	PFAM
Pfam:Collagen	459	523	6.1e-11	PFAM
Pfam:Collagen	548	610	4.5e-11	PFAM
low complexity region	639	661	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000151987

Meta Mutation Damage Score

0.9582

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.6%
20x: 96.0%

Validation Efficiency

93% (38/41)

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, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 94 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700056E22Rik	C	T	1: 183,765,702 (GRCm39)	S119N	probably benign	Het
4930503L19Rik	T	A	18: 70,600,997 (GRCm39)		probably null	Het
Adam18	T	C	8: 25,137,869 (GRCm39)	T324A	probably benign	Het
Adamts20	T	A	15: 94,184,252 (GRCm39)	Q1517L	probably benign	Het
AI429214	A	G	8: 37,461,473 (GRCm39)	Q207R	probably benign	Het
Arhgef7	A	G	8: 11,869,659 (GRCm39)	T432A	possibly damaging	Het
Atad2b	A	G	12: 5,081,784 (GRCm39)	N1231S	probably benign	Het
Atp13a1	T	C	8: 70,254,794 (GRCm39)		probably null	Het
Atp6v0a1	T	A	11: 100,946,317 (GRCm39)	L770*	probably null	Het
Atp8b3	T	C	10: 80,370,032 (GRCm39)	N127S	probably damaging	Het
B3gnt5	T	A	16: 19,588,760 (GRCm39)	D326E	probably damaging	Het
Birc6	T	A	17: 74,872,856 (GRCm39)	S372T	probably damaging	Het
Btbd9	T	A	17: 30,518,607 (GRCm39)	D451V	probably damaging	Het
Cd46	T	C	1: 194,724,300 (GRCm39)	*366W	probably null	Het
Cdcp3	T	C	7: 130,839,911 (GRCm39)	L611P	probably damaging	Het
Cdh18	T	A	15: 23,474,081 (GRCm39)	D650E	probably damaging	Het
Cenpc1	A	T	5: 86,185,767 (GRCm39)	V248E	probably damaging	Het
Cep152	A	G	2: 125,436,819 (GRCm39)	S574P	probably benign	Het
Chd2	A	G	7: 73,128,412 (GRCm39)	S858P	probably damaging	Het
Cib4	T	C	5: 30,645,938 (GRCm39)	D110G	probably damaging	Het
Csmd2	A	T	4: 128,389,981 (GRCm39)	I2239F	possibly damaging	Het
Csmd3	C	A	15: 47,522,485 (GRCm39)	G2728V	probably damaging	Het
Cxcl1	A	T	5: 91,039,626 (GRCm39)	K85*	probably null	Het
Cyp2d11	A	G	15: 82,273,730 (GRCm39)	L416P	possibly damaging	Het
Daam1	A	C	12: 71,962,558 (GRCm39)	K90T	unknown	Het
Depdc5	T	A	5: 33,144,310 (GRCm39)	M1435K	possibly damaging	Het
Dip2c	G	A	13: 9,626,944 (GRCm39)	A632T	probably damaging	Het
Dld	A	T	12: 31,384,053 (GRCm39)	I350N	probably damaging	Het
Dmtf1	T	A	5: 9,177,987 (GRCm39)	I391F	possibly damaging	Het
Dnah14	T	C	1: 181,579,710 (GRCm39)	V3081A	probably damaging	Het
Efemp1	A	G	11: 28,804,538 (GRCm39)	E22G	probably damaging	Het
Ephb6	A	G	6: 41,591,038 (GRCm39)	D65G	probably damaging	Het
Fsip2	A	T	2: 82,807,436 (GRCm39)	T1252S	probably benign	Het
Gm4847	A	G	1: 166,457,824 (GRCm39)	S510P	probably benign	Het
Golga4	T	C	9: 118,366,341 (GRCm39)	I365T	probably damaging	Het
Gp2	A	T	7: 119,053,766 (GRCm39)	L65Q	probably damaging	Het
Ibtk	T	C	9: 85,625,630 (GRCm39)	Y40C	probably damaging	Het
Ice1	C	A	13: 70,750,546 (GRCm39)	V1847L	probably benign	Het
Ift172	C	T	5: 31,422,699 (GRCm39)	R917H	probably benign	Het
Itgae	C	T	11: 73,029,335 (GRCm39)	Q1037*	probably null	Het
Kbtbd7	A	G	14: 79,664,870 (GRCm39)	E234G	possibly damaging	Het
Khsrp	T	C	17: 57,332,576 (GRCm39)	T235A	probably benign	Het
Klk13	T	C	7: 43,370,582 (GRCm39)		probably null	Het
Lrfn5	G	A	12: 61,890,223 (GRCm39)	G504D	probably damaging	Het
Macf1	A	G	4: 123,369,793 (GRCm39)	V91A	possibly damaging	Het
Map6	G	A	7: 98,985,950 (GRCm39)	G821D	possibly damaging	Het
Mark1	A	C	1: 184,653,801 (GRCm39)	V167G	probably damaging	Het
Mrgprf	T	A	7: 144,861,993 (GRCm39)	L185Q	probably damaging	Het
Mtor	T	A	4: 148,634,645 (GRCm39)	V2422D	probably damaging	Het
Myh13	T	A	11: 67,223,346 (GRCm39)	I222N	probably damaging	Het
Myh7b	G	A	2: 155,462,347 (GRCm39)	C350Y	probably benign	Het
Nfix	G	A	8: 85,453,155 (GRCm39)	R300C	probably damaging	Het
Olfm3	C	A	3: 114,895,635 (GRCm39)	S172R	probably benign	Het
Or13e8	A	G	4: 43,696,706 (GRCm39)	S156P	probably damaging	Het
Or1j14	A	G	2: 36,418,020 (GRCm39)	I199V	probably benign	Het
Or4c1	A	T	2: 89,133,528 (GRCm39)	I136N	probably damaging	Het
Or5d40	A	T	2: 88,015,322 (GRCm39)	T34S	probably benign	Het
Or8b48	T	A	9: 38,492,579 (GRCm39)	V2D	possibly damaging	Het
Pacs1	A	T	19: 5,193,857 (GRCm39)	D557E	probably damaging	Het
Pde1c	A	G	6: 56,338,800 (GRCm39)	F11L	probably benign	Het
Phactr2	T	C	10: 13,122,883 (GRCm39)	D343G	possibly damaging	Het
Piezo2	T	C	18: 63,148,873 (GRCm39)	Y2659C	probably damaging	Het
Pkd2l2	A	G	18: 34,561,305 (GRCm39)	T438A	probably damaging	Het
Pld2	T	C	11: 70,447,907 (GRCm39)	W857R	probably damaging	Het
Plxnb1	T	C	9: 108,931,210 (GRCm39)	V410A	possibly damaging	Het
Pramel26	T	C	4: 143,538,428 (GRCm39)	Y181C	probably damaging	Het
Ptger2	A	G	14: 45,226,957 (GRCm39)	Y179C	probably damaging	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Rcan1	A	T	16: 92,190,408 (GRCm39)	M177K	probably benign	Het
Rilpl1	A	G	5: 124,639,934 (GRCm39)	S156P	probably benign	Het
Rilpl1	A	G	5: 124,639,951 (GRCm39)	I122T	possibly damaging	Het
Rims4	C	T	2: 163,705,849 (GRCm39)	V262M	possibly damaging	Het
Rpa1	C	T	11: 75,203,799 (GRCm39)		probably null	Het
Saxo2	A	G	7: 82,284,078 (GRCm39)	V260A	probably benign	Het
Sel1l	T	C	12: 91,791,634 (GRCm39)	Y309C	probably damaging	Het
Setd1b	GCCCCCCC	GCCCCCCCCCCCCC	5: 123,298,766 (GRCm39)		probably benign	Het
Slc33a1	A	G	3: 63,850,725 (GRCm39)	F533S	probably benign	Het
Slc38a4	C	T	15: 96,903,739 (GRCm39)	V421M	probably benign	Het
Snx14	A	G	9: 88,282,774 (GRCm39)		probably null	Het
Spef2	A	G	15: 9,716,482 (GRCm39)	F368S	probably damaging	Het
Sri	A	T	5: 8,109,381 (GRCm39)	Q55L	probably damaging	Het
Stat4	A	G	1: 52,135,979 (GRCm39)	I429M	probably damaging	Het
Stkld1	A	T	2: 26,841,462 (GRCm39)	Q469L	probably benign	Het
Tm9sf1	T	C	14: 55,880,392 (GRCm39)	T2A	possibly damaging	Het
Tmco5	A	G	2: 116,713,699 (GRCm39)	T122A	probably benign	Het
Tmem59l	G	A	8: 70,938,710 (GRCm39)	P124S	possibly damaging	Het
Tmem81	G	A	1: 132,435,662 (GRCm39)	R156Q	probably damaging	Het
Trpv6	T	A	6: 41,602,122 (GRCm39)	T396S	probably benign	Het
Usp24	T	A	4: 106,228,276 (GRCm39)	Y780*	probably null	Het
Utp25	A	T	1: 192,797,011 (GRCm39)	N573K	probably damaging	Het
Vmn1r120	A	G	7: 20,786,941 (GRCm39)	C257R	probably damaging	Het
Vmn2r53	A	G	7: 12,335,319 (GRCm39)	F114L	probably damaging	Het
Vwf	A	G	6: 125,619,969 (GRCm39)	E1549G	probably damaging	Het
Zfp626	G	A	7: 27,517,907 (GRCm39)	R296H	probably damaging	Het

Other mutations in Col9a2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01331:Col9a2	APN	4	120,902,389 (GRCm39)	missense	possibly damaging	0.95
IGL01978:Col9a2	APN	4	120,901,863 (GRCm39)	missense	unknown
IGL01995:Col9a2	APN	4	120,907,607 (GRCm39)	critical splice donor site	probably null
IGL02162:Col9a2	APN	4	120,911,531 (GRCm39)	unclassified	probably benign
IGL02931:Col9a2	APN	4	120,910,389 (GRCm39)	missense	probably benign	0.06
collision	UTSW	4	120,906,913 (GRCm39)	critical splice donor site	probably null
gravity_wave	UTSW	4	120,901,216 (GRCm39)	critical splice donor site	probably null
R0208:Col9a2	UTSW	4	120,909,485 (GRCm39)	splice site	probably benign
R0426:Col9a2	UTSW	4	120,901,857 (GRCm39)	splice site	probably benign
R0512:Col9a2	UTSW	4	120,911,504 (GRCm39)	missense	probably benign	0.22
R1023:Col9a2	UTSW	4	120,901,207 (GRCm39)	missense	unknown
R1657:Col9a2	UTSW	4	120,898,171 (GRCm39)	missense	unknown
R1724:Col9a2	UTSW	4	120,911,099 (GRCm39)	missense	probably damaging	1.00
R2171:Col9a2	UTSW	4	120,902,198 (GRCm39)	nonsense	probably null
R2206:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2221:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2223:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2273:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2274:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2275:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2354:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2392:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2393:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R2394:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R3421:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R3426:Col9a2	UTSW	4	120,907,604 (GRCm39)	missense	possibly damaging	0.93
R3710:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R3821:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R3838:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R3839:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R4067:Col9a2	UTSW	4	120,909,586 (GRCm39)	missense	probably damaging	1.00
R4298:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R4299:Col9a2	UTSW	4	120,911,455 (GRCm39)	missense	probably damaging	0.98
R4595:Col9a2	UTSW	4	120,902,352 (GRCm39)	missense	probably benign	0.04
R4942:Col9a2	UTSW	4	120,910,316 (GRCm39)	missense	possibly damaging	0.73
R5120:Col9a2	UTSW	4	120,896,969 (GRCm39)	missense	unknown
R5434:Col9a2	UTSW	4	120,898,162 (GRCm39)	nonsense	probably null
R6143:Col9a2	UTSW	4	120,911,060 (GRCm39)	missense	probably damaging	0.99
R7027:Col9a2	UTSW	4	120,901,216 (GRCm39)	critical splice donor site	probably null
R7056:Col9a2	UTSW	4	120,906,913 (GRCm39)	critical splice donor site	probably null
R7417:Col9a2	UTSW	4	120,911,489 (GRCm39)	missense	not run
R7571:Col9a2	UTSW	4	120,896,981 (GRCm39)	missense	unknown
R9120:Col9a2	UTSW	4	120,900,951 (GRCm39)	splice site	probably benign
R9341:Col9a2	UTSW	4	120,911,483 (GRCm39)	missense	probably benign	0.03
R9343:Col9a2	UTSW	4	120,911,483 (GRCm39)	missense	probably benign	0.03
R9389:Col9a2	UTSW	4	120,911,948 (GRCm39)	missense	probably benign	0.00
R9527:Col9a2	UTSW	4	120,899,528 (GRCm39)	critical splice donor site	probably null
R9620:Col9a2	UTSW	4	120,910,403 (GRCm39)	critical splice donor site	probably null
R9784:Col9a2	UTSW	4	120,898,226 (GRCm39)	missense	unknown
Z1176:Col9a2	UTSW	4	120,910,994 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ACTCAGAATGCAGACCCAGG -3'
(R):5'- GGACTAGTCAATCTCCCTTCAC -3'

Sequencing Primer
(F):5'- ACAGTGCTCTCAGGTGACAG -3'
(R):5'- AATCTCCCTTCACCGCGAG -3'

Posted On

2014-10-02