Mutagenetix > Incidental Mutation

Incidental Mutation 'R2274:Col9a2'

244954

Institutional Source

Beutler Lab

Gene Symbol

Col9a2

Ensembl Gene

ENSMUSG00000028626

Gene Name

collagen, type IX, alpha 2

Synonyms

Col9a-2

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R2274 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

121039385-121055322 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 121054258 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Glycine at position 599 (R599G)

Ref Sequence

ENSEMBL: ENSMUSP00000030372 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000030372] [ENSMUST00000058754]

AlphaFold

no structure available at present

Predicted Effect

probably damaging
Transcript: ENSMUST00000030372
AA Change: R599G

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: R599G

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

probably benign
Transcript: ENSMUST00000058754

SMART Domains

Protein: ENSMUSP00000053900
Gene: ENSMUSG00000043207

Domain	Start	End	E-Value	Type
Pfam:Peptidase_M48_N	41	225	2.5e-70	PFAM
Pfam:Peptidase_M48	228	473	5.5e-75	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000140119

Meta Mutation Damage Score

0.3183

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.4%

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, 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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2300003K06Rik	A	T	11: 99,837,841	C59S	possibly damaging	Het
Abca5	A	T	11: 110,275,281	N1556K	possibly damaging	Het
Abcb10	G	T	8: 123,982,752	A21E	probably benign	Het
Ackr1	T	C	1: 173,332,485	N156D	probably benign	Het
Adamtsl3	A	T	7: 82,606,558	S1593C	probably benign	Het
Ank3	T	A	10: 69,950,942		probably null	Het
Aqp4	A	G	18: 15,393,480	S315P	probably benign	Het
Atp7b	T	C	8: 22,020,832	I433V	probably benign	Het
Bco1	G	A	8: 117,108,783		probably null	Het
Cacna1g	T	A	11: 94,415,936	E1842V	probably damaging	Het
Calhm3	T	A	19: 47,157,547	Q73L	probably damaging	Het
Car5a	C	T	8: 121,944,669		probably null	Het
Cdk11b	T	A	4: 155,647,594		probably benign	Het
Cdr2	A	T	7: 120,958,509	H264Q	possibly damaging	Het
D7Ertd443e	A	G	7: 134,270,201	S644P	probably damaging	Het
Dnlz	A	T	2: 26,351,471	C82S	probably damaging	Het
Egr4	A	T	6: 85,512,743	F112I	probably damaging	Het
Emilin1	C	T	5: 30,917,738	P441L	possibly damaging	Het
F11	T	C	8: 45,252,147	D119G	possibly damaging	Het
Fat4	T	A	3: 38,995,899	V3970D	possibly damaging	Het
Fbxw5	C	A	2: 25,504,761	C222*	probably null	Het
Fn1	C	T	1: 71,613,943	G1296R	probably null	Het
Ghr	A	G	15: 3,320,025	V557A	probably benign	Het
Gm11568	A	G	11: 99,858,244	S92G	unknown	Het
Gpatch1	A	T	7: 35,288,678	S678T	probably benign	Het
Gpr155	A	G	2: 73,348,135		probably null	Het
Gucy2f	A	T	X: 142,116,273	M697K	probably benign	Het
Hecw1	T	C	13: 14,346,068	T195A	probably benign	Het
Hoxd1	A	G	2: 74,764,157	K252R	probably damaging	Het
Iqck	G	A	7: 118,899,657	D173N	possibly damaging	Het
Irf8	A	G	8: 120,753,527	E168G	probably damaging	Het
Kcnh1	T	G	1: 192,337,521	V358G	probably damaging	Het
Kifap3	T	A	1: 163,868,758	V652D	possibly damaging	Het
L3hypdh	T	C	12: 72,084,858	Y100C	possibly damaging	Het
Map4k1	T	A	7: 29,001,957	H729Q	probably damaging	Het
March1	T	A	8: 66,387,499	N311K	probably benign	Het
Mier2	T	C	10: 79,544,534	I321V	probably damaging	Het
Mta1	C	T	12: 113,128,150	S291L	probably damaging	Het
Myh2	A	G	11: 67,190,358	K1267E	possibly damaging	Het
Nbea	A	T	3: 55,988,085		probably null	Het
Nexmif	T	G	X: 104,087,846	E155A	possibly damaging	Het
Nkpd1	A	G	7: 19,523,897	I534V	probably benign	Het
Nxph1	G	T	6: 9,247,746	C239F	probably damaging	Het
Odc1	A	G	12: 17,548,424	I189V	probably benign	Het
Olfr1170	A	G	2: 88,224,823	F70L	probably benign	Het
Olfr314	T	C	11: 58,786,666	V144A	probably benign	Het
Olfr351	A	T	2: 36,860,101	N82K	probably damaging	Het
Olfr781	T	C	10: 129,333,457	I192T	probably benign	Het
Pcdhb15	T	C	18: 37,475,443	L576P	probably damaging	Het
Raph1	T	C	1: 60,498,500	D499G	probably damaging	Het
Rptor	T	A	11: 119,756,322	C246*	probably null	Het
Rtl1	T	C	12: 109,594,667	E246G	unknown	Het
Setx	GTGGCT	GT	2: 29,154,061	1814	probably null	Het
Slc12a3	T	A	8: 94,333,287	I187N	possibly damaging	Het
Slc46a1	T	G	11: 78,466,423	S101A	probably benign	Het
Slc4a8	A	G	15: 100,807,402	M830V	probably benign	Het
Sned1	T	A	1: 93,281,642		probably null	Het
St3gal6	T	A	16: 58,488,969	E34D	possibly damaging	Het
Tcstv3	C	T	13: 120,317,654	Q30*	probably null	Het
Tex16	T	A	X: 112,121,141	D1112E	probably damaging	Het
Tmcc3	G	A	10: 94,578,915	V160I	probably damaging	Het
Tmf1	T	A	6: 97,163,586	L776F	probably damaging	Het
Tsr1	A	T	11: 74,904,827		probably null	Het
Tyrp1	A	T	4: 80,837,534	E180V	probably damaging	Het
Ubr3	T	C	2: 70,016,341	V1636A	probably benign	Het
Usp1	T	C	4: 98,929,842	L139P	probably damaging	Het
Vmn1r232	A	G	17: 20,914,203	L45P	probably benign	Het
Vmn1r49	G	A	6: 90,072,144	T292I	probably benign	Het
Wdr19	T	A	5: 65,240,991	M853K	possibly damaging	Het
Zkscan8	C	T	13: 21,521,796	M265I	probably benign	Het

Other mutations in Col9a2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01331:Col9a2	APN	4	121045192	missense	possibly damaging	0.95
IGL01978:Col9a2	APN	4	121044666	missense	unknown
IGL01995:Col9a2	APN	4	121050410	critical splice donor site	probably null
IGL02162:Col9a2	APN	4	121054334	unclassified	probably benign
IGL02931:Col9a2	APN	4	121053192	missense	probably benign	0.06
collision	UTSW	4	121049716	critical splice donor site	probably null
gravity_wave	UTSW	4	121044019	critical splice donor site	probably null
R0208:Col9a2	UTSW	4	121052288	splice site	probably benign
R0426:Col9a2	UTSW	4	121044660	splice site	probably benign
R0512:Col9a2	UTSW	4	121054307	missense	probably benign	0.22
R0973:Col9a2	UTSW	4	121039788	critical splice donor site	probably null
R1023:Col9a2	UTSW	4	121044010	missense	unknown
R1657:Col9a2	UTSW	4	121040974	missense	unknown
R1724:Col9a2	UTSW	4	121053902	missense	probably damaging	1.00
R2171:Col9a2	UTSW	4	121045001	nonsense	probably null
R2206:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2221:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2223:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2273:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2275:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2354:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2392:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2393:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R2394:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R3421:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R3426:Col9a2	UTSW	4	121050407	missense	possibly damaging	0.93
R3710:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R3821:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R3838:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R3839:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R4067:Col9a2	UTSW	4	121052389	missense	probably damaging	1.00
R4298:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R4299:Col9a2	UTSW	4	121054258	missense	probably damaging	0.98
R4595:Col9a2	UTSW	4	121045155	missense	probably benign	0.04
R4942:Col9a2	UTSW	4	121053119	missense	possibly damaging	0.73
R5120:Col9a2	UTSW	4	121039772	missense	unknown
R5434:Col9a2	UTSW	4	121040965	nonsense	probably null
R6143:Col9a2	UTSW	4	121053863	missense	probably damaging	0.99
R7027:Col9a2	UTSW	4	121044019	critical splice donor site	probably null
R7056:Col9a2	UTSW	4	121049716	critical splice donor site	probably null
R7417:Col9a2	UTSW	4	121054292	missense	not run
R7571:Col9a2	UTSW	4	121039784	missense	unknown
R9120:Col9a2	UTSW	4	121043754	splice site	probably benign
R9341:Col9a2	UTSW	4	121054286	missense	probably benign	0.03
R9343:Col9a2	UTSW	4	121054286	missense	probably benign	0.03
R9389:Col9a2	UTSW	4	121054751	missense	probably benign	0.00
R9527:Col9a2	UTSW	4	121042331	critical splice donor site	probably null
R9620:Col9a2	UTSW	4	121053206	critical splice donor site	probably null
R9784:Col9a2	UTSW	4	121041029	missense	unknown
Z1176:Col9a2	UTSW	4	121053797	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATACAGAACCTCCCAAATCTTATCTGG -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'

Sequencing Primer
(F):5'- AACCTCCCAAATCTTATCTGGATCTC -3'
(R):5'- AGAGACACCTCCAGCTTGG -3'

Posted On

2014-10-30