Mutagenetix > Incidental Mutation

Incidental Mutation 'R9620:Col9a2'

724700

Institutional Source

Beutler Lab

Gene Symbol

Col9a2

Ensembl Gene

ENSMUSG00000028626

Gene Name

collagen, type IX, alpha 2

Synonyms

Col9a-2

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R9620 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

121039385-121055322 bp(+) (GRCm38)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to A at 121053206 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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.2%

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A630095E13Rik	A	G	9: 36,637,202		probably null	Het
Abhd3	G	T	18: 10,704,605	T151K	possibly damaging	Het
Acsf2	C	T	11: 94,572,586	W130*	probably null	Het
Aldh16a1	G	A	7: 45,147,989	R132*	probably null	Het
Amer3	C	T	1: 34,588,962	P761S	probably benign	Het
Amotl1	G	T	9: 14,548,673	D886E	probably damaging	Het
Cacna1s	T	C	1: 136,108,171	F1383S	probably damaging	Het
Casc4	T	C	2: 121,906,761	V261A	probably benign	Het
Col14a1	T	A	15: 55,362,385	V148E	unknown	Het
Cyp2a5	T	A	7: 26,837,211	M205K	possibly damaging	Het
Dcst2	A	T	3: 89,370,518	Q466L	possibly damaging	Het
Ecel1	T	C	1: 87,153,131	I350V	possibly damaging	Het
Enthd1	G	A	15: 80,452,700	T511I	probably benign	Het
Exoc6b	T	A	6: 85,011,320	K92*	probably null	Het
Fam181a	T	G	12: 103,316,332	Y165*	probably null	Het
Fam205c	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	TCATTCAACACTTTGGAGAGCTCTGAACTCTGGCCATTCAACACTTTGGAGAGCTCTGAACTCTGGTCATTCAACACTTTGG	4: 42,871,823		probably benign	Het
Fam71d	A	C	12: 78,715,303	D247A	probably damaging	Het
Fbxo34	A	G	14: 47,531,268	Y746C	probably damaging	Het
Fgfr4	T	A	13: 55,161,181	S372T	possibly damaging	Het
Fmo1	A	G	1: 162,833,821	F298L	probably benign	Het
Gad1	A	C	2: 70,574,276	D170A	possibly damaging	Het
Golgb1	T	C	16: 36,919,449	S2758P	probably benign	Het
H2afv	A	T	11: 6,429,094		probably null	Het
Ilkap	A	G	1: 91,376,251	C163R		Het
Krt9	A	T	11: 100,188,360	D735E	unknown	Het
Lipo3	A	T	19: 33,582,229	C80*	probably null	Het
Lpcat3	C	T	6: 124,703,580	P478L	probably damaging	Het
Luc7l3	G	A	11: 94,321,719	R24C	unknown	Het
Mafa	T	A	15: 75,747,312	H204L	probably benign	Het
Mapk10	A	C	5: 102,966,607	V305G	probably damaging	Het
Mgat1	T	C	11: 49,261,295	F202L	probably benign	Het
Micalcl	A	T	7: 112,381,196	T126S	probably benign	Het
Mill1	G	A	7: 18,263,102	R206H	probably benign	Het
Nlrc5	A	T	8: 94,476,406	Y378F	probably benign	Het
Nlrp9a	G	T	7: 26,551,044	R78L	probably damaging	Het
Olfr1358	G	T	10: 78,520,294	A229S	probably benign	Het
Olfr150	A	T	9: 39,736,991	M59L		Het
Olfr556	A	T	7: 102,670,804	I295F	possibly damaging	Het
Orc6	A	T	8: 85,299,801		probably benign	Het
Pcdhgb5	C	T	18: 37,731,433	Q94*	probably null	Het
Pcnx	A	G	12: 81,950,186	D952G	probably damaging	Het
Ppfia2	A	T	10: 106,913,658	H1135L		Het
Prmt2	A	T	10: 76,225,379	I91N	probably damaging	Het
Ptprm	A	G	17: 66,809,489	Y932H	probably damaging	Het
Qrich2	T	C	11: 116,447,120	K154R	probably damaging	Het
Rapgef4	A	G	2: 72,205,707	T515A	probably benign	Het
Rgmb	G	A	17: 15,821,017	R103*	probably null	Het
Ripk1	T	G	13: 34,026,823	S334A	possibly damaging	Het
Rnf5	C	T	17: 34,601,747	G147S	possibly damaging	Het
Ryr1	T	C	7: 29,015,713	Y4662C	unknown	Het
Secisbp2l	A	G	2: 125,747,474	M718T	probably damaging	Het
Slc16a6	T	C	11: 109,463,496	T100A	probably benign	Het
Slc27a6	T	A	18: 58,609,815	M525K	probably damaging	Het
Slco2a1	G	C	9: 103,084,866	C579S	probably damaging	Het
Snx14	A	G	9: 88,381,741	S864P	probably damaging	Het
Sptbn2	T	C	19: 4,750,507	L2250P	probably damaging	Het
Tlr6	A	T	5: 64,954,803	S254T	possibly damaging	Het
Trap1	A	T	16: 4,040,219	Y675*	probably null	Het
Ttc9b	C	A	7: 27,654,087	A54E	probably damaging	Het
Unc45a	A	C	7: 80,325,655	Y934D	probably damaging	Het
Usp17ld	A	G	7: 103,250,972	L251P	possibly damaging	Het
Usp42	A	G	5: 143,717,399	V489A	probably damaging	Het
Vars	A	G	17: 35,016,025	T1277A	unknown	Het
Vmn2r117	A	G	17: 23,478,476	S81P	probably damaging	Het
Vmn2r69	T	A	7: 85,412,296	I157F	probably benign	Het
Zfp697	A	G	3: 98,427,866	S316G	probably damaging	Het
Zfp729b	T	A	13: 67,591,668	H826L	probably damaging	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
R2274: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
R9784:Col9a2	UTSW	4	121041029	missense	unknown
Z1176:Col9a2	UTSW	4	121053797	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TTCAGAAGCCTTCTCAGTCCAC -3'
(R):5'- CAATTCAGGAAGAAGCTCTGGC -3'

Sequencing Primer
(F):5'- AGTCCACACCGTCCCCTG -3'
(R):5'- TCTGGCTGCCAAGACCAAC -3'

Posted On

2022-09-12