Mutagenetix > Incidental Mutation

Incidental Mutation 'R8472:Col9a3'

657053

Institutional Source

Beutler Lab

Gene Symbol

Col9a3

Ensembl Gene

ENSMUSG00000027570

Gene Name

collagen, type IX, alpha 3

Synonyms

MMRRC Submission

067916-MU

Accession Numbers

Essential gene?

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

Stock #

R8472 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

180239895-180263985 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 180247057 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 185 (P185L)

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: P185L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: P185L

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

probably damaging
Transcript: ENSMUST00000132527
AA Change: P185L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: P185L

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

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

100% (61/61)

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: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900092C05Rik	T	A	7: 12,246,568 (GRCm39)	H21Q	possibly damaging	Het
Ccdc7a	A	G	8: 129,754,138 (GRCm39)	S152P	probably damaging	Het
Ccnj	T	C	19: 40,833,608 (GRCm39)	S222P	probably damaging	Het
Cdcp2	C	T	4: 106,959,981 (GRCm39)	A132V	probably damaging	Het
Cnksr3	G	T	10: 7,084,532 (GRCm39)	P71Q	probably damaging	Het
Cpm	T	C	10: 117,515,883 (GRCm39)	V319A	probably damaging	Het
Ctxn2	A	G	2: 124,989,528 (GRCm39)	I52V	possibly damaging	Het
Cyp2c66	A	T	19: 39,165,021 (GRCm39)	H334L	probably benign	Het
Dab1	A	G	4: 104,336,439 (GRCm39)	K12E	possibly damaging	Het
Efcab3	A	T	11: 104,709,463 (GRCm39)	D1815V	probably benign	Het
Emsy	T	C	7: 98,304,037 (GRCm39)		probably benign	Het
Etv4	G	T	11: 101,674,827 (GRCm39)	D56E	probably damaging	Het
Exoc3l2	C	T	7: 19,215,190 (GRCm39)	R484*	probably null	Het
Extl1	A	G	4: 134,098,603 (GRCm39)	C143R	probably benign	Het
Fat3	T	C	9: 16,286,563 (GRCm39)	I987V	possibly damaging	Het
Fbn1	A	C	2: 125,151,722 (GRCm39)	C2511G	probably damaging	Het
Fer	T	A	17: 64,280,144 (GRCm39)	S72T	probably benign	Het
Gdf2	A	G	14: 33,666,797 (GRCm39)	D173G	probably damaging	Het
Grhl3	T	C	4: 135,284,176 (GRCm39)	E222G	probably benign	Het
Gria1	A	T	11: 57,218,410 (GRCm39)	M819L	probably benign	Het
Gsap	A	T	5: 21,427,432 (GRCm39)	R187*	probably null	Het
Heatr6	A	G	11: 83,656,679 (GRCm39)	N314D	probably benign	Het
Hspd1	T	C	1: 55,117,505 (GRCm39)	D555G	probably benign	Het
Ighv3-4	T	C	12: 114,217,649 (GRCm39)	Y8C	probably benign	Het
Lcmt2	A	G	2: 120,970,729 (GRCm39)	V118A	probably damaging	Het
Lmf2	T	C	15: 89,239,005 (GRCm39)	E37G	possibly damaging	Het
Macf1	A	G	4: 123,346,795 (GRCm39)	L1161P	probably damaging	Het
Mbip	T	A	12: 56,377,054 (GRCm39)		probably null	Het
Mgam	A	T	6: 40,671,460 (GRCm39)		probably null	Het
Mmrn1	G	A	6: 60,965,380 (GRCm39)	S1136N	probably damaging	Het
Mms22l	T	C	4: 24,502,943 (GRCm39)	V73A	possibly damaging	Het
Mtbp	C	T	15: 55,449,748 (GRCm39)	L24F	probably damaging	Het
Ncr1	T	A	7: 4,341,120 (GRCm39)	I37N	probably benign	Het
Nkx3-1	A	G	14: 69,429,507 (GRCm39)	N175S	probably damaging	Het
Nlrp4f	A	G	13: 65,342,145 (GRCm39)	I500T	possibly damaging	Het
Or10a3	T	A	7: 108,479,973 (GRCm39)	Q280L	possibly damaging	Het
Or1e1f	C	T	11: 73,856,223 (GRCm39)	S263L	possibly damaging	Het
Or6c33	A	G	10: 129,853,445 (GRCm39)	T72A	probably damaging	Het
Pcdha2	A	G	18: 37,074,325 (GRCm39)	D652G	probably damaging	Het
Pde6a	T	A	18: 61,354,018 (GRCm39)	N114K	probably damaging	Het
Pdp2	A	G	8: 105,320,913 (GRCm39)	E254G	probably benign	Het
Pip5kl1	T	C	2: 32,470,018 (GRCm39)	V241A	probably benign	Het
Prkdc	T	A	16: 15,469,400 (GRCm39)	D168E	probably damaging	Het
Psg27	A	T	7: 18,296,015 (GRCm39)	H143Q	probably benign	Het
Serpina16	T	A	12: 103,638,796 (GRCm39)	I264F	probably benign	Het
Slc25a41	G	A	17: 57,348,582 (GRCm39)	H4Y	probably benign	Het
Slco1a8	T	G	6: 141,949,115 (GRCm39)	H87P	probably damaging	Het
Smc3	T	G	19: 53,617,142 (GRCm39)	H518Q	probably benign	Het
Snrpb	G	T	2: 130,015,042 (GRCm39)	T158K	probably damaging	Het
Sobp	A	G	10: 42,898,392 (GRCm39)	F398L	probably damaging	Het
Spidr	T	A	16: 15,958,591 (GRCm39)	Q57L	probably benign	Het
Srd5a3	T	G	5: 76,297,648 (GRCm39)	V26G	possibly damaging	Het
Stx17	A	G	4: 48,166,972 (GRCm39)	T131A	probably benign	Het
Susd1	A	G	4: 59,332,985 (GRCm39)	L553P	possibly damaging	Het
Tbc1d30	C	A	10: 121,187,009 (GRCm39)	G59C	probably benign	Het
Tekt1	T	C	11: 72,242,850 (GRCm39)	D219G	possibly damaging	Het
Trav9d-1	A	T	14: 53,030,163 (GRCm39)	D89V	possibly damaging	Het
Trim34b	T	C	7: 103,980,545 (GRCm39)	I211T	probably benign	Het
Vmn1r25	A	T	6: 57,955,531 (GRCm39)	L253M	possibly damaging	Het
Vmn1r56	C	T	7: 5,198,904 (GRCm39)	V238M	probably damaging	Het
Wipf3	A	G	6: 54,466,070 (GRCm39)	I443V	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
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
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'- AACTGAATGGGGCCCTGTTC -3'
(R):5'- ATCCTCTGATCTCTTAGGCCAG -3'

Sequencing Primer
(F):5'- CAGACTTGTCTCCATCACTAGAGGG -3'
(R):5'- TCACAGCAGCTTCCAGTGTG -3'

Posted On

2021-01-18