Mutagenetix > Incidental Mutation

Incidental Mutation 'R4688:Col9a3'

353821

Institutional Source

Beutler Lab

Gene Symbol

Col9a3

Ensembl Gene

ENSMUSG00000027570

Gene Name

collagen, type IX, alpha 3

Synonyms

MMRRC Submission

041939-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.211) question?

Stock #

R4688 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

180239895-180263985 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 180249424 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 262 (D262G)

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: D262G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: D262G

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: D262G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: D262G

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: ENSMUST00000141056

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 94.3%

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: 96 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700003E16Rik	A	G	6: 83,139,680 (GRCm39)	N535S	probably damaging	Het
Abcc12	T	C	8: 87,275,323 (GRCm39)	S452G	possibly damaging	Het
Acacb	C	A	5: 114,342,824 (GRCm39)	Q897K	probably benign	Het
Acot3	C	A	12: 84,100,691 (GRCm39)	R145S	probably damaging	Het
Ankrd54	A	T	15: 78,938,782 (GRCm39)	Y247N	probably damaging	Het
Arl11	G	A	14: 61,548,546 (GRCm39)	V119I	probably benign	Het
Atosb	A	G	4: 43,034,663 (GRCm39)	F352S	probably damaging	Het
Atxn7	T	A	14: 14,089,288 (GRCm38)	M268K	probably benign	Het
Bms1	G	A	6: 118,369,667 (GRCm39)	R934C	probably damaging	Het
Brd10	A	G	19: 29,694,501 (GRCm39)	I1664T	probably benign	Het
Chrnb3	T	C	8: 27,884,147 (GRCm39)	S295P	probably damaging	Het
Cic	TCCCCC	TCCCCCCC	7: 24,991,095 (GRCm39)		probably null	Het
Cnr1	A	T	4: 33,944,571 (GRCm39)	I320F	probably benign	Het
Cntn4	C	T	6: 106,414,910 (GRCm39)	P147L	probably damaging	Het
Col24a1	G	A	3: 145,020,144 (GRCm39)	V172I	probably benign	Het
Csrnp2	A	G	15: 100,380,241 (GRCm39)	V350A	probably damaging	Het
D630045J12Rik	A	G	6: 38,173,592 (GRCm39)	V192A	possibly damaging	Het
Deptor	A	G	15: 55,072,177 (GRCm39)	M219V	probably benign	Het
Dmrtb1	A	T	4: 107,541,247 (GRCm39)	L38Q	probably damaging	Het
Dvl2	G	A	11: 69,898,344 (GRCm39)	R367Q	possibly damaging	Het
Dync1h1	T	G	12: 110,621,962 (GRCm39)	I3435S	probably damaging	Het
Ecpas	A	G	4: 58,840,757 (GRCm39)	V667A	probably damaging	Het
Eif2b3	A	G	4: 116,916,046 (GRCm39)	N218D	probably benign	Het
Epha2	A	G	4: 141,046,292 (GRCm39)	D497G	probably benign	Het
Epha7	G	T	4: 28,821,367 (GRCm39)	L177F	probably damaging	Het
Fam98c	C	T	7: 28,854,666 (GRCm39)	E147K	probably damaging	Het
Fbxo17	A	G	7: 28,431,979 (GRCm39)	T19A	probably benign	Het
Fbxo47	A	G	11: 97,747,049 (GRCm39)	F339S	probably damaging	Het
Frmd4a	G	T	2: 4,542,122 (GRCm39)	V234L	possibly damaging	Het
Gal3st2	A	G	1: 93,800,245 (GRCm39)	D32G	probably damaging	Het
Gpr135	T	C	12: 72,117,720 (GRCm39)	T16A	probably benign	Het
Gpr160	A	T	3: 30,950,835 (GRCm39)	R302S	probably benign	Het
Hrh2	C	A	13: 54,368,820 (GRCm39)	N265K	probably benign	Het
Htatip2	C	A	7: 49,423,171 (GRCm39)	A242E	probably damaging	Het
Igfbp7	T	C	5: 77,555,482 (GRCm39)	Y127C	probably damaging	Het
Igkv16-104	A	G	6: 68,402,878 (GRCm39)	Q57R	possibly damaging	Het
Ino80c	A	G	18: 24,241,903 (GRCm39)	S161P	probably damaging	Het
Itprid1	G	A	6: 55,944,132 (GRCm39)		probably null	Het
Kcnc1	A	G	7: 46,047,259 (GRCm39)	D53G	probably benign	Het
Khdc4	T	A	3: 88,593,824 (GRCm39)	M71K	probably damaging	Het
Lce1h	G	T	3: 92,670,874 (GRCm39)	R93S	unknown	Het
Lce1k	T	C	3: 92,713,951 (GRCm39)	S78G	unknown	Het
Lhcgr	T	A	17: 89,072,580 (GRCm39)	I156F	probably damaging	Het
Lpl	T	C	8: 69,352,077 (GRCm39)	Y343H	probably damaging	Het
Lrp6	G	T	6: 134,456,706 (GRCm39)	R853S	probably damaging	Het
Lrrc7	A	G	3: 157,854,242 (GRCm39)	V1322A	probably damaging	Het
Lrrc74a	C	T	12: 86,784,472 (GRCm39)	Q67*	probably null	Het
Megf6	A	T	4: 154,338,271 (GRCm39)	D447V	probably damaging	Het
Mep1a	T	C	17: 43,793,139 (GRCm39)	D355G	possibly damaging	Het
Ncoa1	T	C	12: 4,365,781 (GRCm39)	D95G	probably benign	Het
Npepl1	A	T	2: 173,956,235 (GRCm39)	I139F	possibly damaging	Het
Nrcam	T	C	12: 44,594,020 (GRCm39)	S262P	probably benign	Het
Nrp1	A	G	8: 129,229,047 (GRCm39)	N842D	probably benign	Het
Olfml3	A	G	3: 103,639,497 (GRCm39)		probably benign	Het
Or1x6	A	G	11: 50,939,815 (GRCm39)	R294G	probably damaging	Het
Or4b1d	T	A	2: 89,969,343 (GRCm39)	N47Y	possibly damaging	Het
Or6b6	T	A	7: 106,571,068 (GRCm39)	Y161F	probably benign	Het
Or6c204	G	A	10: 129,022,514 (GRCm39)	P259S	probably damaging	Het
Or6k8-ps1	T	C	1: 173,979,162 (GRCm39)	Y27H	possibly damaging	Het
Or8b3b	A	G	9: 38,584,659 (GRCm39)	L27P	probably damaging	Het
Or9i1b	A	T	19: 13,896,605 (GRCm39)	T74S	probably benign	Het
Pde2a	A	G	7: 101,152,041 (GRCm39)	N316S	probably benign	Het
Pde4dip	T	A	3: 97,750,993 (GRCm39)	R74*	probably null	Het
Pex13	A	T	11: 23,605,472 (GRCm39)	W253R	possibly damaging	Het
Piezo1	A	T	8: 123,215,278 (GRCm39)	W1444R	probably damaging	Het
Pla2g4e	T	C	2: 119,998,414 (GRCm39)	K843R	possibly damaging	Het
Plxna2	C	T	1: 194,326,753 (GRCm39)	P229L	probably damaging	Het
Prelid3b	G	T	2: 174,308,592 (GRCm39)	T131K	probably benign	Het
Pros1	T	C	16: 62,709,370 (GRCm39)		probably null	Het
Prrc2c	G	T	1: 162,525,256 (GRCm39)	P450Q	unknown	Het
Ptbp1	G	T	10: 79,692,342 (GRCm39)	V5F	possibly damaging	Het
Ptk2	T	A	15: 73,078,074 (GRCm39)	L997F	probably damaging	Het
Rims1	G	T	1: 22,518,528 (GRCm39)	S525*	probably null	Het
Sanbr	A	G	11: 23,543,449 (GRCm39)	S530P	probably benign	Het
Sh2b3	T	A	5: 121,956,697 (GRCm39)	D318V	probably benign	Het
Slc16a13	A	T	11: 70,111,101 (GRCm39)	I88N	probably damaging	Het
Slit2	T	A	5: 48,414,345 (GRCm39)		probably null	Het
Snx10	A	G	6: 51,556,918 (GRCm39)	N67S	probably damaging	Het
Stil	A	G	4: 114,898,505 (GRCm39)	Y1045C	probably damaging	Het
Stra6	A	G	9: 58,042,359 (GRCm39)		probably null	Het
Sympk	A	G	7: 18,788,335 (GRCm39)	S1254G	probably benign	Het
Syt15	G	T	14: 33,950,011 (GRCm39)	G377V	probably damaging	Het
Taar4	A	T	10: 23,836,731 (GRCm39)	I114F	probably damaging	Het
Tcaf3	G	A	6: 42,570,300 (GRCm39)		probably null	Het
Tgm7	A	T	2: 120,924,502 (GRCm39)	N558K	probably benign	Het
Tln2	T	G	9: 67,304,935 (GRCm39)	M1L	probably benign	Het
Trim50	C	T	5: 135,395,994 (GRCm39)	T314I	probably damaging	Het
Trp53rka	A	T	2: 165,333,312 (GRCm39)	Y192*	probably null	Het
Ube3b	T	C	5: 114,531,139 (GRCm39)	V211A	probably benign	Het
Ush2a	A	G	1: 188,132,138 (GRCm39)	S787G	probably benign	Het
Vmn1r189	T	C	13: 22,286,289 (GRCm39)	M183V	probably damaging	Het
Vps13d	G	T	4: 144,904,782 (GRCm39)	Q115K	probably benign	Het
Zfp358	A	G	8: 3,545,493 (GRCm39)	D25G	probably damaging	Het
Zfp521	T	G	18: 13,977,647 (GRCm39)	K922T	probably damaging	Het
Zfp521	T	A	18: 13,977,648 (GRCm39)	K922*	probably null	Het
Zfp68	T	A	5: 138,614,743 (GRCm39)	K4*	probably null	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
R4731:Col9a3	UTSW	2	180,252,474 (GRCm39)	missense	probably damaging	0.99
R4742:Col9a3	UTSW	2	180,245,180 (GRCm39)	missense	unknown
R4847:Col9a3	UTSW	2	180,257,318 (GRCm39)	missense	probably damaging	1.00
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'- ATCCAGCCTGCATGGGAAATC -3'
(R):5'- GAGCATAGAGAGCCTTCATACCC -3'

Sequencing Primer
(F):5'- TGCATGGGAAATCTGCCTC -3'
(R):5'- TTCATACCCCGGGCAGG -3'

Posted On

2015-10-21