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

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: 99.3%
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
4930548H24Rik	A	G	5: 31,487,526 (GRCm38)	R208G	possibly damaging	Het
Abcc12	T	C	8: 86,531,525 (GRCm38)		probably null	Het
Akna	A	T	4: 63,398,032 (GRCm38)	D31E	possibly damaging	Het
Apbb2	A	T	5: 66,313,378 (GRCm38)	H528Q	probably damaging	Het
Atp6v1g3	C	A	1: 138,283,724 (GRCm38)	Y47*	probably null	Het
AW551984	T	C	9: 39,592,979 (GRCm38)	T564A	probably benign	Het
BC048403	C	A	10: 121,745,446 (GRCm38)	H117Q	probably benign	Het
C4b	T	C	17: 34,731,144 (GRCm38)	D1384G	possibly damaging	Het
C87499	T	C	4: 88,628,182 (GRCm38)	K137E	probably damaging	Het
Cbfa2t2	G	A	2: 154,523,928 (GRCm38)	V353I	probably damaging	Het
Cdh7	T	C	1: 110,061,001 (GRCm38)	I211T	probably damaging	Het
Cep170b	T	C	12: 112,739,305 (GRCm38)	S1166P	probably damaging	Het
Crygs	G	A	16: 22,805,411 (GRCm38)	Q149*	probably null	Het
Cyp2c70	T	C	19: 40,183,928 (GRCm38)	Q90R	probably benign	Het
Cyp3a41b	T	C	5: 145,573,677 (GRCm38)	Y129C	possibly damaging	Het
Dnah10	A	G	5: 124,819,925 (GRCm38)	T3645A	probably damaging	Het
Dolk	A	T	2: 30,285,188 (GRCm38)	W282R	probably damaging	Het
Dsg2	T	A	18: 20,595,951 (GRCm38)		probably null	Het
Dysf	A	G	6: 84,068,077 (GRCm38)	T297A	possibly damaging	Het
Flt1	G	T	5: 147,683,907 (GRCm38)	D142E	probably benign	Het
Frmd4a	C	A	2: 4,333,071 (GRCm38)	N29K	probably benign	Het
Fxyd7	A	T	7: 31,044,982 (GRCm38)	M36K	probably benign	Het
Gabbr1	C	T	17: 37,055,900 (GRCm38)	R178*	probably null	Het
Gm14139	G	A	2: 150,190,733 (GRCm38)	D17N	probably damaging	Het
Gnal	C	G	18: 67,088,583 (GRCm38)	P19R	unknown	Het
Gprc5b	G	A	7: 118,984,214 (GRCm38)	A144V	possibly damaging	Het
Il1rapl1	A	T	X: 87,300,707 (GRCm38)	I194N	probably damaging	Het
Klhl24	T	C	16: 20,107,004 (GRCm38)	M94T	probably damaging	Het
Kmt2e	T	A	5: 23,464,914 (GRCm38)	I133N	probably damaging	Het
Macf1	A	G	4: 123,399,406 (GRCm38)	I5381T	probably damaging	Het
Madd	A	G	2: 91,169,803 (GRCm38)	L197P	probably damaging	Het
Mapkapk3	G	A	9: 107,257,449 (GRCm38)	T296M	probably damaging	Het
Micall2	T	C	5: 139,709,471 (GRCm38)		probably benign	Het
Myh9	T	C	15: 77,769,964 (GRCm38)	T1214A	probably benign	Het
Ncapd3	A	G	9: 27,052,327 (GRCm38)	N492S	probably benign	Het
Neurl4	A	C	11: 69,909,061 (GRCm38)	D1055A	probably damaging	Het
Nrbp1	T	C	5: 31,250,599 (GRCm38)		probably null	Het
Olfr1052	A	T	2: 86,298,241 (GRCm38)	I142F	possibly damaging	Het
Olfr27	T	C	9: 39,144,999 (GRCm38)	S300P	probably benign	Het
Olfr380	A	T	11: 73,454,001 (GRCm38)	D70E	probably damaging	Het
Olfr421-ps1	T	A	1: 174,152,312 (GRCm38)	Y265*	probably null	Het
Olfr53	T	C	7: 140,652,243 (GRCm38)	V88A	probably benign	Het
Olfr67	T	A	7: 103,787,995 (GRCm38)	H94L	probably benign	Het
Olfr901	T	G	9: 38,430,812 (GRCm38)	Y177D	probably damaging	Het
Olfr933	T	A	9: 38,975,759 (GRCm38)	F28I	probably damaging	Het
Patj	C	A	4: 98,677,321 (GRCm38)	N1090K	possibly damaging	Het
Pde8a	A	G	7: 81,328,035 (GRCm38)	D692G	probably benign	Het
Ppa2	G	T	3: 133,367,842 (GRCm38)	K220N	probably damaging	Het
Rad54b	A	G	4: 11,597,865 (GRCm38)	H250R	probably damaging	Het
Reln	A	C	5: 21,920,487 (GRCm38)	C2733G	probably damaging	Het
Rgs14	A	G	13: 55,383,753 (GRCm38)	T497A	probably damaging	Het
Rpl13-ps3	T	A	14: 58,893,523 (GRCm38)		noncoding transcript	Het
Scn11a	T	G	9: 119,765,506 (GRCm38)	I1274L	probably damaging	Het
Sco1	A	T	11: 67,055,800 (GRCm38)	H133L	possibly damaging	Het
Slc4a8	T	C	15: 100,796,640 (GRCm38)		probably null	Het
Smc2	C	T	4: 52,440,238 (GRCm38)		probably benign	Het
Spata18	T	C	5: 73,666,902 (GRCm38)	I156T	probably benign	Het
St3gal2	T	C	8: 110,962,359 (GRCm38)	M177T	probably benign	Het
Stt3a	A	G	9: 36,763,344 (GRCm38)	F48L	probably damaging	Het
Syvn1	C	T	19: 6,049,921 (GRCm38)		probably benign	Het
Szt2	A	G	4: 118,365,406 (GRCm38)		probably benign	Het
Telo2	A	T	17: 25,115,256 (GRCm38)	S6T	possibly damaging	Het
Tnfrsf11b	T	C	15: 54,252,095 (GRCm38)	M369V	probably benign	Het
Tnfrsf13b	C	G	11: 61,140,817 (GRCm38)		probably null	Het
Vmn1r234	A	T	17: 21,229,021 (GRCm38)	M66L	probably benign	Het
Vmn2r12	C	A	5: 109,091,964 (GRCm38)	M244I	probably benign	Het
Wdfy2	T	A	14: 62,925,140 (GRCm38)	L97*	probably null	Het
Wdr63	C	T	3: 146,068,806 (GRCm38)	D429N	probably damaging	Het
Xrcc5	T	C	1: 72,394,720 (GRCm38)	*733Q	probably null	Het
Zadh2	A	T	18: 84,094,501 (GRCm38)	I101F	possibly damaging	Het
Zfp516	G	A	18: 82,987,497 (GRCm38)	G842D	possibly damaging	Het
Zwilch	A	G	9: 64,155,162 (GRCm38)		probably null	Het

Other mutations in Col9a2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01331:Col9a2	APN	4	121,045,192 (GRCm38)	missense	possibly damaging	0.95
IGL01978:Col9a2	APN	4	121,044,666 (GRCm38)	missense	unknown
IGL01995:Col9a2	APN	4	121,050,410 (GRCm38)	critical splice donor site	probably null
IGL02162:Col9a2	APN	4	121,054,334 (GRCm38)	unclassified	probably benign
IGL02931:Col9a2	APN	4	121,053,192 (GRCm38)	missense	probably benign	0.06
collision	UTSW	4	121,049,716 (GRCm38)	critical splice donor site	probably null
gravity_wave	UTSW	4	121,044,019 (GRCm38)	critical splice donor site	probably null
R0208:Col9a2	UTSW	4	121,052,288 (GRCm38)	splice site	probably benign
R0426:Col9a2	UTSW	4	121,044,660 (GRCm38)	splice site	probably benign
R0512:Col9a2	UTSW	4	121,054,307 (GRCm38)	missense	probably benign	0.22
R0973:Col9a2	UTSW	4	121,039,788 (GRCm38)	critical splice donor site	probably null
R1023:Col9a2	UTSW	4	121,044,010 (GRCm38)	missense	unknown
R1657:Col9a2	UTSW	4	121,040,974 (GRCm38)	missense	unknown
R1724:Col9a2	UTSW	4	121,053,902 (GRCm38)	missense	probably damaging	1.00
R2171:Col9a2	UTSW	4	121,045,001 (GRCm38)	nonsense	probably null
R2206:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2221:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2223:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2273:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2274:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2275:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2354:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2392:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2393:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R2394:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R3421:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R3426:Col9a2	UTSW	4	121,050,407 (GRCm38)	missense	possibly damaging	0.93
R3710:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R3821:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R3838:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R3839:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R4067:Col9a2	UTSW	4	121,052,389 (GRCm38)	missense	probably damaging	1.00
R4298:Col9a2	UTSW	4	121,054,258 (GRCm38)	missense	probably damaging	0.98
R4595:Col9a2	UTSW	4	121,045,155 (GRCm38)	missense	probably benign	0.04
R4942:Col9a2	UTSW	4	121,053,119 (GRCm38)	missense	possibly damaging	0.73
R5120:Col9a2	UTSW	4	121,039,772 (GRCm38)	missense	unknown
R5434:Col9a2	UTSW	4	121,040,965 (GRCm38)	nonsense	probably null
R6143:Col9a2	UTSW	4	121,053,863 (GRCm38)	missense	probably damaging	0.99
R7027:Col9a2	UTSW	4	121,044,019 (GRCm38)	critical splice donor site	probably null
R7056:Col9a2	UTSW	4	121,049,716 (GRCm38)	critical splice donor site	probably null
R7417:Col9a2	UTSW	4	121,054,292 (GRCm38)	missense	not run
R7571:Col9a2	UTSW	4	121,039,784 (GRCm38)	missense	unknown
R9120:Col9a2	UTSW	4	121,043,754 (GRCm38)	splice site	probably benign
R9341:Col9a2	UTSW	4	121,054,286 (GRCm38)	missense	probably benign	0.03
R9343:Col9a2	UTSW	4	121,054,286 (GRCm38)	missense	probably benign	0.03
R9389:Col9a2	UTSW	4	121,054,751 (GRCm38)	missense	probably benign	0.00
R9527:Col9a2	UTSW	4	121,042,331 (GRCm38)	critical splice donor site	probably null
R9620:Col9a2	UTSW	4	121,053,206 (GRCm38)	critical splice donor site	probably null
R9784:Col9a2	UTSW	4	121,041,029 (GRCm38)	missense	unknown
Z1176:Col9a2	UTSW	4	121,053,797 (GRCm38)	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