Mutagenetix > Incidental Mutation

Incidental Mutation 'R4299:Col9a2'

323471

Institutional Source

Beutler Lab

Gene Symbol

Col9a2

Ensembl Gene

ENSMUSG00000028626

Gene Name

collagen, type IX, alpha 2

Synonyms

Col9a-2

MMRRC Submission

041087-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4299 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120896763-120912522 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to G at 120911455 bp (GRCm39)

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: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.4%

Validation Efficiency

97% (76/78)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc12	T	C	8: 87,258,154 (GRCm39)		probably null	Het
Akna	A	T	4: 63,316,269 (GRCm39)	D31E	possibly damaging	Het
Apbb2	A	T	5: 66,470,721 (GRCm39)	H528Q	probably damaging	Het
Atp6v1g3	C	A	1: 138,211,462 (GRCm39)	Y47*	probably null	Het
AW551984	T	C	9: 39,504,275 (GRCm39)	T564A	probably benign	Het
C4b	T	C	17: 34,950,118 (GRCm39)	D1384G	possibly damaging	Het
Cbfa2t2	G	A	2: 154,365,848 (GRCm39)	V353I	probably damaging	Het
Ccdc121	A	G	5: 31,644,870 (GRCm39)	R208G	possibly damaging	Het
Cdh20	T	C	1: 109,988,731 (GRCm39)	I211T	probably damaging	Het
Cep170b	T	C	12: 112,705,739 (GRCm39)	S1166P	probably damaging	Het
Crygs	G	A	16: 22,624,161 (GRCm39)	Q149*	probably null	Het
Cyp2c70	T	C	19: 40,172,372 (GRCm39)	Q90R	probably benign	Het
Cyp3a41b	T	C	5: 145,510,487 (GRCm39)	Y129C	possibly damaging	Het
Dnah10	A	G	5: 124,896,989 (GRCm39)	T3645A	probably damaging	Het
Dnai3	C	T	3: 145,774,561 (GRCm39)	D429N	probably damaging	Het
Dolk	A	T	2: 30,175,200 (GRCm39)	W282R	probably damaging	Het
Dsg2	T	A	18: 20,729,008 (GRCm39)		probably null	Het
Dysf	A	G	6: 84,045,059 (GRCm39)	T297A	possibly damaging	Het
Flt1	G	T	5: 147,620,717 (GRCm39)	D142E	probably benign	Het
Frmd4a	C	A	2: 4,337,882 (GRCm39)	N29K	probably benign	Het
Fxyd7	A	T	7: 30,744,407 (GRCm39)	M36K	probably benign	Het
Gabbr1	C	T	17: 37,366,792 (GRCm39)	R178*	probably null	Het
Gnal	C	G	18: 67,221,654 (GRCm39)	P19R	unknown	Het
Gprc5b	G	A	7: 118,583,437 (GRCm39)	A144V	possibly damaging	Het
Il1rapl1	A	T	X: 86,344,313 (GRCm39)	I194N	probably damaging	Het
Kics2	C	A	10: 121,581,351 (GRCm39)	H117Q	probably benign	Het
Klhl24	T	C	16: 19,925,754 (GRCm39)	M94T	probably damaging	Het
Kmt2e	T	A	5: 23,669,912 (GRCm39)	I133N	probably damaging	Het
Macf1	A	G	4: 123,293,199 (GRCm39)	I5381T	probably damaging	Het
Madd	A	G	2: 91,000,148 (GRCm39)	L197P	probably damaging	Het
Mapkapk3	G	A	9: 107,134,648 (GRCm39)	T296M	probably damaging	Het
Micall2	T	C	5: 139,695,226 (GRCm39)		probably benign	Het
Myh9	T	C	15: 77,654,164 (GRCm39)	T1214A	probably benign	Het
Ncapd3	A	G	9: 26,963,623 (GRCm39)	N492S	probably benign	Het
Neurl4	A	C	11: 69,799,887 (GRCm39)	D1055A	probably damaging	Het
Nrbp1	T	C	5: 31,407,943 (GRCm39)		probably null	Het
Or13a20	T	C	7: 140,232,156 (GRCm39)	V88A	probably benign	Het
Or1e21	A	T	11: 73,344,827 (GRCm39)	D70E	probably damaging	Het
Or52z1	T	A	7: 103,437,202 (GRCm39)	H94L	probably benign	Het
Or5j3	A	T	2: 86,128,585 (GRCm39)	I142F	possibly damaging	Het
Or6k8-ps1	T	A	1: 173,979,878 (GRCm39)	Y265*	probably null	Het
Or8b42	T	G	9: 38,342,108 (GRCm39)	Y177D	probably damaging	Het
Or8d1b	T	A	9: 38,887,055 (GRCm39)	F28I	probably damaging	Het
Or8g19	T	C	9: 39,056,295 (GRCm39)	S300P	probably benign	Het
Patj	C	A	4: 98,565,558 (GRCm39)	N1090K	possibly damaging	Het
Pde8a	A	G	7: 80,977,783 (GRCm39)	D692G	probably benign	Het
Ppa2	G	T	3: 133,073,603 (GRCm39)	K220N	probably damaging	Het
Pramel32	T	C	4: 88,546,419 (GRCm39)	K137E	probably damaging	Het
Ptgr3	A	T	18: 84,112,626 (GRCm39)	I101F	possibly damaging	Het
Rad54b	A	G	4: 11,597,865 (GRCm39)	H250R	probably damaging	Het
Reln	A	C	5: 22,125,485 (GRCm39)	C2733G	probably damaging	Het
Rgs14	A	G	13: 55,531,566 (GRCm39)	T497A	probably damaging	Het
Rpl13-ps3	T	A	14: 59,130,972 (GRCm39)		noncoding transcript	Het
Scn11a	T	G	9: 119,594,572 (GRCm39)	I1274L	probably damaging	Het
Sco1	A	T	11: 66,946,626 (GRCm39)	H133L	possibly damaging	Het
Slc4a8	T	C	15: 100,694,521 (GRCm39)		probably null	Het
Smc2	C	T	4: 52,440,238 (GRCm39)		probably benign	Het
Spata18	T	C	5: 73,824,245 (GRCm39)	I156T	probably benign	Het
St3gal2	T	C	8: 111,688,991 (GRCm39)	M177T	probably benign	Het
Stt3a	A	G	9: 36,674,640 (GRCm39)	F48L	probably damaging	Het
Syvn1	C	T	19: 6,099,951 (GRCm39)		probably benign	Het
Szt2	A	G	4: 118,222,603 (GRCm39)		probably benign	Het
Telo2	A	T	17: 25,334,230 (GRCm39)	S6T	possibly damaging	Het
Tnfrsf11b	T	C	15: 54,115,491 (GRCm39)	M369V	probably benign	Het
Tnfrsf13b	C	G	11: 61,031,643 (GRCm39)		probably null	Het
Vmn1r234	A	T	17: 21,449,283 (GRCm39)	M66L	probably benign	Het
Vmn2r12	C	A	5: 109,239,830 (GRCm39)	M244I	probably benign	Het
Wdfy2	T	A	14: 63,162,589 (GRCm39)	L97*	probably null	Het
Xrcc5	T	C	1: 72,433,879 (GRCm39)	*733Q	probably null	Het
Zfp1004	G	A	2: 150,032,653 (GRCm39)	D17N	probably damaging	Het
Zfp516	G	A	18: 83,005,622 (GRCm39)	G842D	possibly damaging	Het
Zwilch	A	G	9: 64,062,444 (GRCm39)		probably null	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
R0973:Col9a2	UTSW	4	120,896,985 (GRCm39)	critical splice donor site	probably null
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
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'- AACCTCCCAAATCTTATCTGGATC -3'
(R):5'- TCAAGAGTCCCAACTGCCAG -3'

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

Posted On

2015-06-20