Mutagenetix > Incidental Mutation

Incidental Mutation 'R4571:Col9a3'

342127

Institutional Source

Beutler Lab

Gene Symbol

Col9a3

Ensembl Gene

ENSMUSG00000027570

Gene Name

collagen, type IX, alpha 3

Synonyms

MMRRC Submission

041795-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.222) question?

Stock #

R4571 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

180597790-180622189 bp(+) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

T to C at 180616366 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000128718 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000103059] [ENSMUST00000132527]

AlphaFold

A2ACT7

Predicted Effect

probably benign
Transcript: ENSMUST00000103059

SMART Domains

Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570

Domain	Start	End	E-Value	Type
Pfam:Collagen	21	80	7.7e-12	PFAM
Pfam:Collagen	58	114	4.2e-9	PFAM
low complexity region	126	162	N/A	INTRINSIC
Pfam:Collagen	174	236	4.1e-12	PFAM
Pfam:Collagen	213	292	8e-9	PFAM
internal_repeat_1	315	366	1.58e-12	PROSPERO
internal_repeat_2	360	382	2.94e-6	PROSPERO
low complexity region	384	396	N/A	INTRINSIC
Pfam:Collagen	456	518	1.8e-11	PFAM
Pfam:Collagen	545	606	3.8e-11	PFAM
low complexity region	635	656	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000129090

Predicted Effect

probably benign
Transcript: ENSMUST00000132527

SMART Domains

Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570

Domain	Start	End	E-Value	Type
Pfam:Collagen	21	80	7.9e-12	PFAM
Pfam:Collagen	58	114	4.3e-9	PFAM
Pfam:Collagen	109	166	4.5e-8	PFAM
Pfam:Collagen	174	236	4.2e-12	PFAM
Pfam:Collagen	213	292	8.2e-9	PFAM
internal_repeat_1	315	366	1.58e-12	PROSPERO
internal_repeat_2	360	382	2.94e-6	PROSPERO
low complexity region	384	396	N/A	INTRINSIC
Pfam:Collagen	402	474	8.2e-8	PFAM
Pfam:Collagen	456	518	1.8e-11	PFAM
Pfam:Collagen	545	606	3.9e-11	PFAM
Pfam:Collagen	603	662	2.5e-8	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165224

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165879

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.3%

Validation Efficiency

100% (69/69)

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. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]

Allele List at MGI

Other mutations in this stock

Total: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700123L14Rik	T	A	6: 96,164,881	N394I	probably damaging	Het
Abca8a	A	T	11: 110,030,058	C1497S	probably damaging	Het
Acoxl	G	T	2: 127,877,807	G163W	probably damaging	Het
Apbb1	T	A	7: 105,573,762	N214I	probably damaging	Het
Apol7b	T	C	15: 77,423,534	K254E	probably benign	Het
Arl4d	T	A	11: 101,667,143	V165E	possibly damaging	Het
Brca1	C	A	11: 101,517,366	R1377L	probably benign	Het
Btf3	A	G	13: 98,313,284	F65L	probably benign	Het
C2	T	C	17: 34,863,659	N495D	probably benign	Het
Cacna1c	T	C	6: 118,630,380	T1188A	probably benign	Het
Chd7	C	A	4: 8,866,217	D796E	probably benign	Het
Clasp2	G	T	9: 113,847,721	L173F	probably damaging	Het
Clec4g	A	T	8: 3,718,766		probably null	Het
Csmd2	T	A	4: 128,480,095		probably null	Het
Ddx11	T	C	17: 66,130,773	C165R	probably benign	Het
Dnah7c	A	C	1: 46,533,216	M950L	probably damaging	Het
Dusp23	A	C	1: 172,632,614		probably null	Het
Ebag9	A	T	15: 44,636,762		probably null	Het
Edn3	G	A	2: 174,781,904	A211T	probably benign	Het
Eif3e	G	A	15: 43,266,162	T190I	possibly damaging	Het
Fam76a	T	C	4: 132,920,897	H3R	possibly damaging	Het
Gabbr1	G	T	17: 37,054,236	E138*	probably null	Het
Galc	T	C	12: 98,222,617	T412A	probably benign	Het
Gimap3	T	C	6: 48,765,720	D92G	possibly damaging	Het
Gin1	T	C	1: 97,785,076	Y285H	probably damaging	Het
Gm4868	A	G	5: 125,848,718		noncoding transcript	Het
Gm7052	T	A	17: 22,040,424		probably benign	Het
Gpcpd1	T	A	2: 132,550,350	E226D	probably benign	Het
Hoxb4	T	C	11: 96,319,166	S133P	possibly damaging	Het
Hrg	C	T	16: 22,961,222		probably benign	Het
Insrr	A	G	3: 87,800,887	K212R	probably benign	Het
Ipp	A	G	4: 116,530,458	D411G	probably damaging	Het
Kcnd3	C	T	3: 105,658,766	A421V	probably damaging	Het
Kcnq3	A	G	15: 66,030,612	F172L	probably damaging	Het
Kdm5d	T	C	Y: 927,110	F616S	probably damaging	Het
Lars	T	C	18: 42,228,230		probably null	Het
Lmo7	G	T	14: 101,887,594	Q496H	probably damaging	Het
Map3k9	C	A	12: 81,734,091	A432S	probably benign	Het
Nop2	T	G	6: 125,140,881		probably null	Het
Olfr1029	A	T	2: 85,975,831	E196V	probably damaging	Het
Olfr1115	C	A	2: 87,252,458	Q174K	possibly damaging	Het
Olfr420	A	T	1: 174,158,928	N52Y	possibly damaging	Het
Olfr90	T	C	17: 37,085,579	I195M	probably damaging	Het
Pan2	A	G	10: 128,308,643	T187A	probably benign	Het
Pcmtd2	A	G	2: 181,842,424	E9G	possibly damaging	Het
Pik3cb	T	A	9: 99,090,257	I283F	possibly damaging	Het
Pkhd1	G	A	1: 20,613,409	T40I	probably damaging	Het
Plxna2	T	C	1: 194,810,988	V1857A	possibly damaging	Het
Polg	T	C	7: 79,460,379	S334G	probably damaging	Het
Rem2	T	C	14: 54,477,659	S98P	probably damaging	Het
Rpl5-ps2	G	T	2: 154,704,236		noncoding transcript	Het
Slc6a18	A	T	13: 73,666,370	N468K	possibly damaging	Het
Slco4a1	A	T	2: 180,464,378	T118S	probably benign	Het
Smg1	A	T	7: 118,139,465	N3520K	possibly damaging	Het
Tapbp	C	A	17: 33,926,453	D415E	probably damaging	Het
Topaz1	A	G	9: 122,747,436	T31A	probably benign	Het
Trpv6	C	T	6: 41,621,744	R649H	probably damaging	Het
Vmn1r188	A	G	13: 22,088,518	Y214C	probably benign	Het
Vps8	T	A	16: 21,435,775	I59N	probably damaging	Het
Wnt9a	T	C	11: 59,331,337	C354R	probably damaging	Het
Zcchc2	A	G	1: 106,031,257	T1153A	possibly damaging	Het
Zfp30	A	G	7: 29,793,202	R294G	probably damaging	Het
Zfp558	A	T	9: 18,456,503	C330S	possibly damaging	Het
Zfp62	A	C	11: 49,215,741	S220R	probably damaging	Het
Zfp62	G	T	11: 49,215,742	S220I	probably damaging	Het
Zp3r	A	G	1: 130,578,020	S423P	probably damaging	Het

Other mutations in Col9a3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01022:Col9a3	APN	2	180616434	missense	probably damaging	0.96
IGL01542:Col9a3	APN	2	180609316	splice site	probably benign
IGL01727:Col9a3	APN	2	180616565	critical splice donor site	probably null
IGL02558:Col9a3	APN	2	180606806	critical splice acceptor site	probably null
IGL03112:Col9a3	APN	2	180607642	missense	possibly damaging	0.60
IGL02796:Col9a3	UTSW	2	180614162	missense	probably damaging	1.00
R0022:Col9a3	UTSW	2	180619756	missense	probably damaging	1.00
R0022:Col9a3	UTSW	2	180619756	missense	probably damaging	1.00
R0046:Col9a3	UTSW	2	180609487	missense	possibly damaging	0.47
R0046:Col9a3	UTSW	2	180609487	missense	possibly damaging	0.47
R0477:Col9a3	UTSW	2	180609470	splice site	probably benign
R0890:Col9a3	UTSW	2	180610063	missense	probably benign	0.23
R1934:Col9a3	UTSW	2	180607134	missense	probably damaging	0.98
R4355:Col9a3	UTSW	2	180606478	missense	probably benign	0.00
R4688:Col9a3	UTSW	2	180607631	missense	probably damaging	0.99
R4731:Col9a3	UTSW	2	180610681	missense	probably damaging	0.99
R4742:Col9a3	UTSW	2	180603387	missense	unknown
R4847:Col9a3	UTSW	2	180615525	missense	probably damaging	1.00
R4985:Col9a3	UTSW	2	180603400	missense	unknown
R5488:Col9a3	UTSW	2	180616525	missense	probably damaging	1.00
R5489:Col9a3	UTSW	2	180616525	missense	probably damaging	1.00
R5573:Col9a3	UTSW	2	180619732	missense	probably benign	0.17
R5575:Col9a3	UTSW	2	180598846	intron	probably benign
R6820:Col9a3	UTSW	2	180607134	missense	probably damaging	0.98
R7114:Col9a3	UTSW	2	180603797	missense	unknown
R7710:Col9a3	UTSW	2	180609365	missense	probably damaging	0.98
R8177:Col9a3	UTSW	2	180607657	missense	probably damaging	0.97
R8342:Col9a3	UTSW	2	180603390	missense	unknown
R8472:Col9a3	UTSW	2	180605264	missense	probably damaging	1.00
R8783:Col9a3	UTSW	2	180614177	missense	probably damaging	0.98
R9683:Col9a3	UTSW	2	180606529	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TTCCAGCATGTGAGATAGTCC -3'
(R):5'- ACCATGCCTTGCTTGAATCAAC -3'

Sequencing Primer
(F):5'- TTCCAGCATGTGAGATAGTCCAAGAG -3'
(R):5'- AGGATCTCCTAGTTCCCCAGTGG -3'

Posted On

2015-09-24