Mutagenetix > Incidental Mutation

Incidental Mutation 'R4847:Col9a3'

373290

Institutional Source

Beutler Lab

Gene Symbol

Col9a3

Ensembl Gene

ENSMUSG00000027570

Gene Name

collagen, type IX, alpha 3

Synonyms

MMRRC Submission

042460-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.186) question?

Stock #

R4847 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

180239895-180263985 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 180257318 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Serine at position 480 (G480S)

Ref Sequence

ENSEMBL: ENSMUSP00000128718 (fasta)

Gene Model

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

AlphaFold

A2ACT7

Predicted Effect

probably damaging
Transcript: ENSMUST00000103059
AA Change: G480S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: G480S

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 damaging
Transcript: ENSMUST00000132527
AA Change: G480S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: G480S

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: 99.1%
3x: 98.4%
10x: 96.7%
20x: 93.7%

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. 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: 63 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
5730455P16Rik	C	T	11: 80,264,940 (GRCm39)	V171M	probably damaging	Het
Abhd3	A	G	18: 10,647,786 (GRCm39)	S328P	possibly damaging	Het
Acot11	C	T	4: 106,617,327 (GRCm39)	G240R	probably damaging	Het
Aldh1b1	G	T	4: 45,802,625 (GRCm39)	K54N	possibly damaging	Het
Amacr	C	T	15: 10,994,958 (GRCm39)	Q257*	probably null	Het
Ankrd12	A	T	17: 66,331,087 (GRCm39)	D309E	probably benign	Het
Anks6	T	C	4: 47,033,266 (GRCm39)	T600A	probably benign	Het
Ap3b1	A	G	13: 94,608,287 (GRCm39)	E586G	probably benign	Het
Atad2b	A	G	12: 4,994,901 (GRCm39)		probably null	Het
Cant1	G	A	11: 118,300,936 (GRCm39)	Q240*	probably null	Het
Cep152	T	C	2: 125,460,394 (GRCm39)	Y186C	possibly damaging	Het
Cep76	C	A	18: 67,752,639 (GRCm39)	R603I	probably benign	Het
Chad	T	C	11: 94,459,153 (GRCm39)	S352P	probably benign	Het
Ckap2	T	C	8: 22,665,084 (GRCm39)	E460G	probably damaging	Het
Col22a1	T	C	15: 71,671,348 (GRCm39)	Y1004C	unknown	Het
Cpsf2	A	G	12: 101,963,561 (GRCm39)	D430G	probably benign	Het
Cramp1	T	C	17: 25,204,063 (GRCm39)	D305G	probably damaging	Het
Ctnnd1	C	A	2: 84,452,396 (GRCm39)	E76*	probably null	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Cyp2c39	A	T	19: 39,549,340 (GRCm39)	N286I	probably damaging	Het
Ddx11	A	G	17: 66,437,796 (GRCm39)	E174G	probably damaging	Het
Ddx19a	T	C	8: 111,703,677 (GRCm39)	E369G	probably damaging	Het
Dnai7	T	A	6: 145,120,911 (GRCm39)	H636L	probably damaging	Het
Epha1	T	A	6: 42,338,848 (GRCm39)	D687V	possibly damaging	Het
Fgr	T	C	4: 132,721,959 (GRCm39)	W132R	probably damaging	Het
Fras1	A	T	5: 96,692,851 (GRCm39)	D170V	possibly damaging	Het
Gas2l1	A	G	11: 5,014,173 (GRCm39)	S96P	probably damaging	Het
Gfy	G	A	7: 44,827,020 (GRCm39)	P359S	probably damaging	Het
Hexim2	A	G	11: 103,029,767 (GRCm39)	N273S	probably benign	Het
Hr	A	T	14: 70,793,916 (GRCm39)	T59S	probably benign	Het
Ift70a2	A	T	2: 75,808,058 (GRCm39)	N151K	probably benign	Het
Impdh2	A	G	9: 108,441,870 (GRCm39)	Y166C	probably damaging	Het
Impdh2	T	A	9: 108,442,714 (GRCm39)	F514Y	probably benign	Het
Iqgap2	A	G	13: 95,810,251 (GRCm39)	F731S	probably benign	Het
Klhl17	A	T	4: 156,316,054 (GRCm39)	H433Q	probably damaging	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Kntc1	A	C	5: 123,940,337 (GRCm39)	N1645T	probably benign	Het
Mcm8	A	G	2: 132,661,923 (GRCm39)	I114V	probably benign	Het
Mink1	T	A	11: 70,492,854 (GRCm39)	L160Q	probably damaging	Het
Mipol1	A	T	12: 57,350,282 (GRCm39)	S27C	probably damaging	Het
Mthfr	T	C	4: 148,132,596 (GRCm39)	V217A	probably damaging	Het
Or5b105	A	G	19: 13,079,898 (GRCm39)	Y257H	probably damaging	Het
Or5p53	T	A	7: 107,533,034 (GRCm39)	C102*	probably null	Het
Pde1c	T	C	6: 56,100,019 (GRCm39)	K614E	possibly damaging	Het
Pds5b	A	T	5: 150,671,577 (GRCm39)	E407V	probably damaging	Het
Pdzph1	A	G	17: 59,280,525 (GRCm39)	S586P	possibly damaging	Het
Prkcb	C	T	7: 122,167,372 (GRCm39)	R361W	probably benign	Het
Psen2	T	A	1: 180,073,197 (GRCm39)		probably null	Het
Ptk2	T	A	15: 73,103,805 (GRCm39)	M82L	probably benign	Het
Ptk2b	T	C	14: 66,411,331 (GRCm39)	D400G	probably damaging	Het
Samd8	G	A	14: 21,842,503 (GRCm39)	R275Q	possibly damaging	Het
Senp2	A	G	16: 21,857,386 (GRCm39)	T403A	possibly damaging	Het
Serpinb13	C	T	1: 106,910,574 (GRCm39)	S66L	probably damaging	Het
Skap2	T	A	6: 51,980,649 (GRCm39)	I52L	probably benign	Het
Slc5a7	T	C	17: 54,584,168 (GRCm39)	D374G	possibly damaging	Het
Slmap	A	T	14: 26,147,763 (GRCm39)	L699M	possibly damaging	Het
Sntg1	A	C	1: 8,665,706 (GRCm39)	C203G	possibly damaging	Het
Stard9	T	C	2: 120,533,594 (GRCm39)	S3284P	probably benign	Het
Tbx21	T	C	11: 97,005,857 (GRCm39)	Y36C	probably damaging	Het
Tecpr2	A	G	12: 110,906,311 (GRCm39)	Y971C	probably damaging	Het
Trpm5	T	A	7: 142,641,500 (GRCm39)	I137F	possibly damaging	Het
Unk	A	G	11: 115,945,232 (GRCm39)	K426E	probably damaging	Het
Zc3hc1	T	C	6: 30,375,981 (GRCm39)	D193G	probably benign	Het

Other mutations in Col9a3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01022:Col9a3	APN	2	180,258,227 (GRCm39)	missense	probably damaging	0.96
IGL01542:Col9a3	APN	2	180,251,109 (GRCm39)	splice site	probably benign
IGL01727:Col9a3	APN	2	180,258,358 (GRCm39)	critical splice donor site	probably null
IGL02558:Col9a3	APN	2	180,248,599 (GRCm39)	critical splice acceptor site	probably null
IGL03112:Col9a3	APN	2	180,249,435 (GRCm39)	missense	possibly damaging	0.60
IGL02796:Col9a3	UTSW	2	180,255,955 (GRCm39)	missense	probably damaging	1.00
R0022:Col9a3	UTSW	2	180,261,549 (GRCm39)	missense	probably damaging	1.00
R0022:Col9a3	UTSW	2	180,261,549 (GRCm39)	missense	probably damaging	1.00
R0046:Col9a3	UTSW	2	180,251,280 (GRCm39)	missense	possibly damaging	0.47
R0046:Col9a3	UTSW	2	180,251,280 (GRCm39)	missense	possibly damaging	0.47
R0477:Col9a3	UTSW	2	180,251,263 (GRCm39)	splice site	probably benign
R0890:Col9a3	UTSW	2	180,251,856 (GRCm39)	missense	probably benign	0.23
R1934:Col9a3	UTSW	2	180,248,927 (GRCm39)	missense	probably damaging	0.98
R4355:Col9a3	UTSW	2	180,248,271 (GRCm39)	missense	probably benign	0.00
R4571:Col9a3	UTSW	2	180,258,159 (GRCm39)	splice site	probably benign
R4688:Col9a3	UTSW	2	180,249,424 (GRCm39)	missense	probably damaging	0.99
R4731:Col9a3	UTSW	2	180,252,474 (GRCm39)	missense	probably damaging	0.99
R4742:Col9a3	UTSW	2	180,245,180 (GRCm39)	missense	unknown
R4985:Col9a3	UTSW	2	180,245,193 (GRCm39)	missense	unknown
R5488:Col9a3	UTSW	2	180,258,318 (GRCm39)	missense	probably damaging	1.00
R5489:Col9a3	UTSW	2	180,258,318 (GRCm39)	missense	probably damaging	1.00
R5573:Col9a3	UTSW	2	180,261,525 (GRCm39)	missense	probably benign	0.17
R5575:Col9a3	UTSW	2	180,240,639 (GRCm39)	intron	probably benign
R6820:Col9a3	UTSW	2	180,248,927 (GRCm39)	missense	probably damaging	0.98
R7114:Col9a3	UTSW	2	180,245,590 (GRCm39)	missense	unknown
R7710:Col9a3	UTSW	2	180,251,158 (GRCm39)	missense	probably damaging	0.98
R8177:Col9a3	UTSW	2	180,249,450 (GRCm39)	missense	probably damaging	0.97
R8342:Col9a3	UTSW	2	180,245,183 (GRCm39)	missense	unknown
R8472:Col9a3	UTSW	2	180,247,057 (GRCm39)	missense	probably damaging	1.00
R8783:Col9a3	UTSW	2	180,255,970 (GRCm39)	missense	probably damaging	0.98
R9683:Col9a3	UTSW	2	180,248,322 (GRCm39)	critical splice donor site	probably null

Predicted Primers

PCR Primer
(F):5'- TTATCCAAGGAGCCCACAGG -3'
(R):5'- AGTGCACCAGTAGTTCTGACC -3'

Sequencing Primer
(F):5'- GGCTCCCATCCACCTCTGTAAG -3'
(R):5'- GCACCAGTAGTTCTGACCTACCTAG -3'

Posted On

2016-03-01