Mutagenetix > Incidental Mutation

Incidental Mutation 'R4355:Col9a3'

327473

Institutional Source

Beutler Lab

Gene Symbol

Col9a3

Ensembl Gene

ENSMUSG00000027570

Gene Name

collagen, type IX, alpha 3

Synonyms

MMRRC Submission

041108-MU

Accession Numbers

Essential gene?

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

Stock #

R4355 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

180239895-180263985 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 180248271 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Glycine at position 208 (S208G)

Ref Sequence

ENSEMBL: ENSMUSP00000128718 (fasta)

Gene Model

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

AlphaFold

A2ACT7

Predicted Effect

probably benign
Transcript: ENSMUST00000103059
AA Change: S208G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: S208G

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
AA Change: S208G

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)

SMART Domains

Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: S208G

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

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

100% (57/57)

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: 52 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam26a	T	G	8: 44,023,222 (GRCm39)	Q89H	probably benign	Het
Adgrb1	T	C	15: 74,415,511 (GRCm39)	F697S	probably damaging	Het
Adgrl2	A	T	3: 148,544,788 (GRCm39)	V769E	probably damaging	Het
Aldh7a1	A	T	18: 56,681,566 (GRCm39)	F173L	probably null	Het
Bcl3	G	T	7: 19,545,505 (GRCm39)	C208*	probably null	Het
Bmal1	A	G	7: 112,902,613 (GRCm39)	I421V	possibly damaging	Het
Casz1	T	C	4: 149,036,792 (GRCm39)	S1685P	unknown	Het
Cep250	A	G	2: 155,833,445 (GRCm39)	E1789G	probably damaging	Het
Cep76	A	T	18: 67,759,710 (GRCm39)	D334E	probably benign	Het
Clca3b	A	T	3: 144,531,219 (GRCm39)		probably null	Het
Ddx47	T	C	6: 134,998,468 (GRCm39)	V388A	probably benign	Het
Dync1h1	C	T	12: 110,599,333 (GRCm39)	A1896V	possibly damaging	Het
Eif2ak2	T	A	17: 79,165,963 (GRCm39)	R411S	probably benign	Het
F7	A	G	8: 13,084,774 (GRCm39)	T267A	probably benign	Het
Fras1	C	A	5: 96,848,101 (GRCm39)	D1770E	probably benign	Het
G2e3	T	A	12: 51,412,120 (GRCm39)	Y387N	probably benign	Het
Hspg2	C	T	4: 137,256,729 (GRCm39)	L1491F	probably damaging	Het
Ighv3-4	T	C	12: 114,217,260 (GRCm39)	I110M	probably benign	Het
Itgb5	T	A	16: 33,665,367 (GRCm39)	C28S	probably damaging	Het
Itprid2	A	G	2: 79,472,342 (GRCm39)	N132S	probably benign	Het
Kbtbd11	C	A	8: 15,078,578 (GRCm39)	N392K	probably damaging	Het
Kcnmb4	A	G	10: 116,309,189 (GRCm39)	S80P	possibly damaging	Het
Kif21a	C	T	15: 90,855,036 (GRCm39)	C721Y	probably benign	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Klrc3	T	C	6: 129,616,125 (GRCm39)	M189V	probably benign	Het
Macf1	T	A	4: 123,368,884 (GRCm39)	E394V	possibly damaging	Het
Mrgprb4	C	T	7: 47,848,449 (GRCm39)	G160R	possibly damaging	Het
Myb	A	G	10: 21,028,516 (GRCm39)	S116P	probably damaging	Het
Nf2	G	A	11: 4,730,613 (GRCm39)	Q513*	probably null	Het
Nmnat3	C	T	9: 98,292,205 (GRCm39)	T150M	possibly damaging	Het
Obi1	A	G	14: 104,716,693 (GRCm39)	V560A	probably benign	Het
Or11g27	T	C	14: 50,771,216 (GRCm39)	C116R	possibly damaging	Het
Or12k8	C	A	2: 36,974,942 (GRCm39)	V273F	probably benign	Het
Patj	T	G	4: 98,538,691 (GRCm39)	C210W	possibly damaging	Het
Pde3b	A	G	7: 114,015,522 (GRCm39)	H246R	probably benign	Het
Pnp2	A	G	14: 51,197,082 (GRCm39)	H56R	probably benign	Het
Prkg1	A	G	19: 30,546,629 (GRCm39)		probably benign	Het
Rhbdf1	C	T	11: 32,166,236 (GRCm39)	S8N	probably damaging	Het
Rimbp3	A	G	16: 17,027,556 (GRCm39)	K327E	possibly damaging	Het
Rsph6a	T	A	7: 18,801,003 (GRCm39)		probably null	Het
Ryr2	T	C	13: 11,664,698 (GRCm39)	N3535S	probably benign	Het
Ston1	T	G	17: 88,944,436 (GRCm39)	V614G	probably damaging	Het
Svep1	T	A	4: 58,138,695 (GRCm39)	T466S	possibly damaging	Het
Tas2r109	A	T	6: 132,957,144 (GRCm39)	I262N	probably benign	Het
Tmtc1	T	C	6: 148,256,596 (GRCm39)		probably benign	Het
Tshz2	G	A	2: 169,726,858 (GRCm39)	E16K	possibly damaging	Het
Ufsp2	T	A	8: 46,438,502 (GRCm39)	S193R	possibly damaging	Het
Ugt2b5	C	A	5: 87,287,622 (GRCm39)	E182*	probably null	Het
Usp43	A	G	11: 67,782,290 (GRCm39)	V376A	probably benign	Het
Utp15	A	T	13: 98,395,755 (GRCm39)	F76I	possibly damaging	Het
Wdr62	A	C	7: 29,941,673 (GRCm39)	L1141R	probably damaging	Het
Zfp418	T	A	7: 7,175,161 (GRCm39)	M18K	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
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
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'- GAGGTCACCATAATTTAGGTTGCC -3'
(R):5'- AACGTGCCTGACATCAGCTG -3'

Sequencing Primer
(F):5'- GCCTTTTTACAGCTATAGGCAAG -3'
(R):5'- AACACTAGCCTTGGTGTCAG -3'

Posted On

2015-07-07