Mutagenetix > Incidental Mutation

Incidental Mutation 'R0512:Col9a2'

47888

Institutional Source

Beutler Lab

Gene Symbol

Col9a2

Ensembl Gene

ENSMUSG00000028626

Gene Name

collagen, type IX, alpha 2

Synonyms

Col9a-2

MMRRC Submission

038706-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R0512 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

120896763-120912522 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 120911504 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Methionine to Lysine at position 615 (M615K)

Ref Sequence

ENSEMBL: ENSMUSP00000030372 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000030372
AA Change: M615K

PolyPhen 2 Score 0.225 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000030372
Gene: ENSMUSG00000028626
AA Change: M615K

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

0.1562

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.7%
20x: 93.8%

Validation Efficiency

100% (92/92)

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: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930519G04Rik	T	G	5: 115,001,569 (GRCm39)	M22R	probably benign	Het
Abca8b	C	A	11: 109,841,476 (GRCm39)	M1039I	probably benign	Het
Actn2	A	T	13: 12,292,301 (GRCm39)	I653N	probably damaging	Het
Actr8	G	T	14: 29,700,513 (GRCm39)	V31L	probably benign	Het
Adam30	T	C	3: 98,069,441 (GRCm39)	C425R	probably damaging	Het
Armc1	A	G	3: 19,203,659 (GRCm39)	V89A	possibly damaging	Het
Atr	T	C	9: 95,817,579 (GRCm39)	M2090T	probably damaging	Het
Braf	T	A	6: 39,641,923 (GRCm39)		probably benign	Het
Cant1	A	T	11: 118,302,091 (GRCm39)	N75K	probably benign	Het
Chd7	C	T	4: 8,805,139 (GRCm39)		probably benign	Het
Clec16a	A	G	16: 10,432,444 (GRCm39)	Y488C	probably damaging	Het
Col6a3	A	T	1: 90,749,520 (GRCm39)		probably benign	Het
Dedd	G	A	1: 171,168,498 (GRCm39)	R228H	probably damaging	Het
Dhtkd1	C	T	2: 5,908,902 (GRCm39)	D731N	probably damaging	Het
Ercc2	A	G	7: 19,127,812 (GRCm39)	T651A	probably damaging	Het
Fam13a	T	A	6: 58,933,684 (GRCm39)	D302V	probably damaging	Het
Fam193a	T	C	5: 34,583,735 (GRCm39)	S19P	probably damaging	Het
Fam43a	T	C	16: 30,420,553 (GRCm39)	V379A	possibly damaging	Het
Fat1	C	A	8: 45,404,369 (GRCm39)	Y373*	probably null	Het
Fbxl15	A	C	19: 46,317,861 (GRCm39)	D181A	probably damaging	Het
Flt3	A	T	5: 147,278,080 (GRCm39)	C831*	probably null	Het
Foxj3	T	A	4: 119,443,033 (GRCm39)		probably benign	Het
Glul	T	C	1: 153,781,132 (GRCm39)		probably benign	Het
Gm16380	A	T	9: 53,791,529 (GRCm39)		noncoding transcript	Het
Gm7964	A	T	7: 83,405,158 (GRCm39)		noncoding transcript	Het
Hipk1	A	G	3: 103,667,890 (GRCm39)	F559S	possibly damaging	Het
Hnf4g	A	T	3: 3,716,682 (GRCm39)	I284F	probably damaging	Het
Hoxa13	CCG	CCGCG	6: 52,237,618 (GRCm39)		probably null	Het
Icosl	A	G	10: 77,907,800 (GRCm39)	N120S	possibly damaging	Het
Ift172	A	G	5: 31,442,821 (GRCm39)	V155A	possibly damaging	Het
Kdm4c	A	G	4: 74,252,031 (GRCm39)	E426G	probably benign	Het
Kif23	A	G	9: 61,826,257 (GRCm39)		probably benign	Het
Krt81	C	A	15: 101,361,508 (GRCm39)	R24L	possibly damaging	Het
Lama1	G	A	17: 68,086,129 (GRCm39)	C1456Y	possibly damaging	Het
Lamc3	T	A	2: 31,827,980 (GRCm39)	L1378Q	probably damaging	Het
Larp1b	T	A	3: 40,924,469 (GRCm39)	L121M	probably benign	Het
Lepr	T	A	4: 101,649,216 (GRCm39)	D872E	probably damaging	Het
Lepr	A	C	4: 101,671,901 (GRCm39)	D975A	possibly damaging	Het
Magi1	A	G	6: 93,671,045 (GRCm39)	V1068A	probably damaging	Het
Malt1	T	A	18: 65,591,271 (GRCm39)	N358K	probably damaging	Het
Mfap4	T	A	11: 61,378,771 (GRCm39)	W240R	probably damaging	Het
Mis18a	A	G	16: 90,523,244 (GRCm39)	V84A	possibly damaging	Het
Mns1	A	G	9: 72,356,753 (GRCm39)	E308G	possibly damaging	Het
Mpp2	C	A	11: 101,953,116 (GRCm39)	L258F	possibly damaging	Het
Myh2	A	G	11: 67,079,504 (GRCm39)	E987G	probably damaging	Het
Myof	A	G	19: 37,942,972 (GRCm39)	V702A	possibly damaging	Het
Nhs	C	A	X: 160,620,355 (GRCm39)	R1467I	probably damaging	Het
Nrxn2	A	G	19: 6,567,228 (GRCm39)	T1360A	probably damaging	Het
Obox6	A	G	7: 15,567,874 (GRCm39)	I191T	probably benign	Het
Pacs2	G	T	12: 113,014,547 (GRCm39)	R236L	probably damaging	Het
Pcdhb2	T	G	18: 37,429,032 (GRCm39)	V335G	probably damaging	Het
Phyhipl	T	C	10: 70,404,748 (GRCm39)	I140M	probably damaging	Het
Pkhd1	T	C	1: 20,380,738 (GRCm39)		probably benign	Het
Ppp1r3b	T	G	8: 35,851,571 (GRCm39)	C137G	probably damaging	Het
Prdm13	T	A	4: 21,678,490 (GRCm39)	I667F	probably damaging	Het
Prex2	A	G	1: 11,270,157 (GRCm39)	M1281V	probably benign	Het
Rab40b	A	G	11: 121,250,412 (GRCm39)	F81L	probably damaging	Het
Rb1cc1	T	C	1: 6,318,767 (GRCm39)	S729P	probably damaging	Het
Rcl1	A	G	19: 29,105,497 (GRCm39)	D228G	probably damaging	Het
Rhbdf1	A	T	11: 32,160,875 (GRCm39)	C19*	probably null	Het
Rif1	GCCACCA	GCCA	2: 52,000,336 (GRCm39)		probably benign	Het
Rnf150	G	A	8: 83,590,807 (GRCm39)	V57M	probably benign	Het
Rp9	A	G	9: 22,370,015 (GRCm39)	F51L	probably benign	Het
Sav1	A	T	12: 70,015,975 (GRCm39)	Y274*	probably null	Het
Scn4a	A	T	11: 106,236,503 (GRCm39)	D252E	probably damaging	Het
Scn5a	T	C	9: 119,379,724 (GRCm39)	T187A	probably damaging	Het
Sigirr	T	A	7: 140,672,333 (GRCm39)	D229V	probably benign	Het
Slc39a13	T	C	2: 90,896,031 (GRCm39)	S157G	possibly damaging	Het
Slc6a20a	A	G	9: 123,489,471 (GRCm39)	S191P	probably damaging	Het
Sorl1	C	A	9: 41,979,128 (GRCm39)	A457S	probably benign	Het
Spag5	A	G	11: 78,210,412 (GRCm39)		probably benign	Het
Spon1	A	G	7: 113,436,066 (GRCm39)	E119G	possibly damaging	Het
Spred2	T	A	11: 19,958,485 (GRCm39)		probably benign	Het
Sprr3	T	G	3: 92,364,784 (GRCm39)	Q20P	possibly damaging	Het
Strn3	A	T	12: 51,673,966 (GRCm39)	F464L	possibly damaging	Het
Sun1	A	G	5: 139,220,602 (GRCm39)		probably benign	Het
Sypl2	A	G	3: 108,133,486 (GRCm39)	W28R	possibly damaging	Het
Syt5	A	T	7: 4,545,813 (GRCm39)	V150D	probably damaging	Het
Tasor	T	C	14: 27,168,363 (GRCm39)	F302L	probably damaging	Het
Thsd7a	A	G	6: 12,379,604 (GRCm39)	I940T	possibly damaging	Het
Tlcd3b	C	T	7: 126,426,795 (GRCm39)	R73C	probably damaging	Het
Tnrc6a	T	A	7: 122,785,951 (GRCm39)		probably benign	Het
Trp53	T	A	11: 69,479,509 (GRCm39)	L203Q	probably damaging	Het
Tubgcp4	T	C	2: 121,005,900 (GRCm39)	V96A	probably benign	Het
Usp17la	A	G	7: 104,510,246 (GRCm39)	T284A	possibly damaging	Het
Usp34	T	C	11: 23,401,997 (GRCm39)	M2409T	probably benign	Het
Vmn2r100	C	A	17: 19,742,382 (GRCm39)	P252Q	possibly damaging	Het
Vmn2r56	A	G	7: 12,449,350 (GRCm39)	I296T	probably benign	Het
Vmn2r67	A	G	7: 84,799,900 (GRCm39)	V446A	probably damaging	Het
Zfp217	C	T	2: 169,957,382 (GRCm39)	A539T	probably benign	Het
Zfp267	T	C	3: 36,220,262 (GRCm39)	C762R	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
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
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'- AGATTGGCAACACTGGACCCAAG -3'
(R):5'- TGCCAGACTCAAGAGTCCCAACTG -3'

Sequencing Primer
(F):5'- TCAAGGTCAGCTTGGTACATAG -3'
(R):5'- GAGTCCCAACTGCCAGC -3'

Posted On

2013-06-12