Mutagenetix > Incidental Mutation

Incidental Mutation 'R7027:Col9a2'

546027

Institutional Source

Beutler Lab

Gene Symbol

Col9a2

Ensembl Gene

ENSMUSG00000028626

Gene Name

collagen, type IX, alpha 2

Synonyms

Col9a-2

MMRRC Submission

045128-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7027 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

121039385-121055322 bp(+) (GRCm38)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 121044019 bp (GRCm38)

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

Meta Mutation Damage Score

0.9491

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.8%
20x: 99.2%

Validation Efficiency

98% (85/87)

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: 88 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acoxl	A	T	2: 128,010,083 (GRCm38)	M102L	probably benign	Het
Adcy10	A	G	1: 165,518,246 (GRCm38)	E288G	probably damaging	Het
Agap1	A	G	1: 89,888,722 (GRCm38)	H748R	probably benign	Het
Ahsg	T	C	16: 22,892,257 (GRCm38)	L48P	probably damaging	Het
Ankrd27	A	G	7: 35,612,526 (GRCm38)	T394A	probably benign	Het
Apc	T	G	18: 34,312,076 (GRCm38)	V657G	probably damaging	Het
Arl2	T	C	19: 6,141,089 (GRCm38)	T5A	probably benign	Het
B020011L13Rik	A	G	1: 117,801,450 (GRCm38)	Y229C	probably benign	Het
B3gnt5	T	A	16: 19,769,990 (GRCm38)	S320T	probably damaging	Het
Bach1	G	A	16: 87,719,291 (GRCm38)	R240Q	probably benign	Het
BC107364	T	G	3: 96,440,741 (GRCm38)	R77S	unknown	Het
Brox	G	A	1: 183,284,186 (GRCm38)	P206L	possibly damaging	Het
Ccrl2	T	C	9: 111,055,885 (GRCm38)	K182E	probably benign	Het
Cd19	A	G	7: 126,410,499 (GRCm38)	V465A	possibly damaging	Het
Chrdl2	A	T	7: 100,022,033 (GRCm38)	Q126H	probably damaging	Het
Cnbd1	G	A	4: 18,862,063 (GRCm38)	P376S	probably benign	Het
Cobll1	A	G	2: 65,089,503 (GRCm38)	S1194P	probably benign	Het
Col6a4	T	C	9: 106,067,014 (GRCm38)	Y1087C	probably damaging	Het
Cyp4v3	A	G	8: 45,310,252 (GRCm38)	S341P	possibly damaging	Het
Dnah7a	T	A	1: 53,631,506 (GRCm38)	Y529F	probably benign	Het
Eif3b	C	T	5: 140,425,288 (GRCm38)	R165W	probably damaging	Het
Erlec1	C	A	11: 30,950,790 (GRCm38)	C126F	probably damaging	Het
Fads2b	A	G	2: 85,485,527 (GRCm38)	Y440H	probably damaging	Het
Fat2	T	C	11: 55,269,433 (GRCm38)	T3285A	probably benign	Het
Fat2	G	A	11: 55,281,851 (GRCm38)	R2679*	probably null	Het
Fbxo31	T	C	8: 121,578,485 (GRCm38)	T91A	probably damaging	Het
Fkbp5	A	G	17: 28,412,063 (GRCm38)	Y243H	probably damaging	Het
Flcn	C	T	11: 59,795,806 (GRCm38)	V374M	probably damaging	Het
Fndc5	A	G	4: 129,139,523 (GRCm38)	M128V	probably benign	Het
Gal3st1	A	G	11: 3,999,002 (GRCm38)	D403G	probably damaging	Het
Garem1	T	C	18: 21,129,994 (GRCm38)	N588D	probably benign	Het
Gas1	T	C	13: 60,176,233 (GRCm38)	T196A	probably damaging	Het
Gcn1	T	C	5: 115,616,546 (GRCm38)		probably null	Het
Gprc5d	T	G	6: 135,116,648 (GRCm38)	Q87P	probably damaging	Het
Grm1	A	G	10: 10,719,595 (GRCm38)	L763P	probably damaging	Het
Hivep2	G	T	10: 14,149,577 (GRCm38)	K2378N	probably damaging	Het
Hivep2	G	T	10: 14,149,578 (GRCm38)	D2379Y	probably damaging	Het
Itgad	A	G	7: 128,182,989 (GRCm38)	Y199C	probably damaging	Het
Itm2c	A	G	1: 85,906,485 (GRCm38)	I174V	probably benign	Het
Khdrbs2	A	G	1: 32,414,916 (GRCm38)	S128G	probably benign	Het
Map3k9	T	C	12: 81,730,624 (GRCm38)	T528A	probably benign	Het
Mmp11	G	A	10: 75,932,396 (GRCm38)		probably benign	Het
Mycbpap	T	A	11: 94,514,614 (GRCm38)	I30F	probably damaging	Het
Nfya	T	C	17: 48,389,312 (GRCm38)	T335A	probably benign	Het
Npat	T	A	9: 53,569,916 (GRCm38)	S1008T	possibly damaging	Het
Or10al5	G	A	17: 37,752,409 (GRCm38)	C185Y	probably damaging	Het
Or12e10	A	G	2: 87,810,716 (GRCm38)	T299A	possibly damaging	Het
Or5p69	A	T	7: 108,368,350 (GRCm38)	M287L	probably damaging	Het
Or6c219	C	T	10: 129,945,172 (GRCm38)	A297T	possibly damaging	Het
Osbpl10	T	C	9: 115,223,698 (GRCm38)	V613A	probably damaging	Het
Pcdhga8	T	C	18: 37,727,111 (GRCm38)	W407R	probably benign	Het
Pcdhgb4	A	G	18: 37,721,362 (GRCm38)	D270G	probably damaging	Het
Pde2a	A	C	7: 101,511,597 (GRCm38)	E918D	probably damaging	Het
Plekhg5	A	G	4: 152,113,974 (GRCm38)	D873G	probably benign	Het
Pno1	A	T	11: 17,208,880 (GRCm38)	S173T	possibly damaging	Het
Ppfia3	A	G	7: 45,354,736 (GRCm38)	I494T	possibly damaging	Het
Prkrip1	C	A	5: 136,181,413 (GRCm38)		probably benign	Het
Psma5	A	G	3: 108,265,168 (GRCm38)	I67V	probably benign	Het
Reep6	G	A	10: 80,333,965 (GRCm38)		probably null	Het
Rtl1	CTCTTCTTCTTCACCATCTTCCTCCTCCTCCCCTTCTTCTTCTTCACCATCTTCCTCCTCCTCCCCTTCTTCTTCTTCACCATCTTCCTCCTCCTC	CTCTTCTTCTTCACCATCTTCCTCCTCCTCCCCTTCTTCTTCTTCACCATCTTCCTCCTCCTC	12: 109,591,414 (GRCm38)		probably benign	Het
Scyl2	C	G	10: 89,645,461 (GRCm38)		probably null	Het
Sdk1	T	A	5: 142,096,726 (GRCm38)		probably null	Het
Senp5	C	A	16: 31,989,295 (GRCm38)	K380N	probably benign	Het
Slc22a14	A	T	9: 119,231,215 (GRCm38)		probably null	Het
Slc26a5	T	A	5: 21,816,974 (GRCm38)	T485S	possibly damaging	Het
Slc44a5	T	C	3: 154,253,719 (GRCm38)	I349T	probably benign	Het
Smarca5	T	C	8: 80,736,726 (GRCm38)	E71G	probably benign	Het
Smok2a	A	T	17: 13,225,779 (GRCm38)	H81L	probably damaging	Het
Snrnp200	A	G	2: 127,217,272 (GRCm38)	D388G	probably benign	Het
Tank	T	C	2: 61,653,422 (GRCm38)	V404A	probably benign	Het
Tek	A	G	4: 94,865,510 (GRCm38)	D1063G	probably damaging	Het
Tfap2a	C	T	13: 40,733,674 (GRCm38)	C16Y	probably benign	Het
Tmc1	A	G	19: 20,940,903 (GRCm38)		probably null	Het
Tnc	A	G	4: 63,984,589 (GRCm38)	F1484L	probably benign	Het
Tnfsf13	T	A	11: 69,685,132 (GRCm38)		probably null	Het
Tnrc6c	T	A	11: 117,733,618 (GRCm38)	S919T	probably damaging	Het
Trim17	C	A	11: 58,968,616 (GRCm38)	Q219K	probably benign	Het
Trim5	T	A	7: 104,265,668 (GRCm38)	H389L	probably benign	Het
Trio	T	A	15: 27,805,654 (GRCm38)	M583L	possibly damaging	Het
Ttll10	A	T	4: 156,035,801 (GRCm38)	H389Q	possibly damaging	Het
Usp24	T	C	4: 106,362,244 (GRCm38)	S546P	probably benign	Het
Vmn1r19	T	A	6: 57,404,490 (GRCm38)	Y9*	probably null	Het
Vmn2r50	T	A	7: 10,047,612 (GRCm38)	D402V	probably damaging	Het
Vmn2r93	C	A	17: 18,313,286 (GRCm38)	A484E	probably benign	Het
Vps13a	T	C	19: 16,664,664 (GRCm38)	T2200A	probably benign	Het
Wdr36	T	A	18: 32,841,905 (GRCm38)	H103Q	probably benign	Het
Zfp534	G	A	4: 147,675,210 (GRCm38)	T334I	possibly damaging	Het
Zfp804b	C	T	5: 6,770,372 (GRCm38)	S897N	probably benign	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
R4299: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
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'- TCTCATTACTCCTGCAGGGC -3'
(R):5'- TGTCCCAGATGCCTCACAAG -3'

Sequencing Primer
(F):5'- CTCCTGCAGGGCCAGCC -3'
(R):5'- GGTAGGGACAAAAGTTTCTTCACTG -3'

Posted On

2019-05-13