Mutagenetix > Incidental Mutation

Incidental Mutation 'R8342:Col9a3'

644935

Institutional Source

Beutler Lab

Gene Symbol

Col9a3

Ensembl Gene

ENSMUSG00000027570

Gene Name

collagen, type IX, alpha 3

Synonyms

MMRRC Submission

067731-MU

Accession Numbers

Essential gene?

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

Stock #

R8342 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

180239895-180263985 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 180245183 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 131 (I131F)

Ref Sequence

ENSEMBL: ENSMUSP00000099348 (fasta)

Gene Model

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

AlphaFold

A2ACT7

Predicted Effect

unknown
Transcript: ENSMUST00000103059
AA Change: I131F

SMART Domains

Protein: ENSMUSP00000099348
Gene: ENSMUSG00000027570
AA Change: I131F

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

unknown
Transcript: ENSMUST00000132527
AA Change: I131F

SMART Domains

Protein: ENSMUSP00000128718
Gene: ENSMUSG00000027570
AA Change: I131F

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: 99.9%
10x: 99.6%
20x: 98.6%

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: 62 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aak1	A	G	6: 86,963,321 (GRCm39)	D917G	unknown	Het
Adad1	T	C	3: 37,134,050 (GRCm39)	S322P	probably damaging	Het
Agbl4	C	T	4: 110,976,224 (GRCm39)	L194F	probably damaging	Het
Ahr	C	T	12: 35,558,271 (GRCm39)	G250R	probably damaging	Het
AI987944	A	T	7: 41,024,310 (GRCm39)	I226N	probably benign	Het
Ankar	A	G	1: 72,691,619 (GRCm39)	V1114A	probably damaging	Het
Ankrd49	C	A	9: 14,692,823 (GRCm39)	A114S	probably damaging	Het
Arl6	C	T	16: 59,442,802 (GRCm39)	G140D	unknown	Het
Arrdc3	A	G	13: 81,031,790 (GRCm39)	S8G	probably benign	Het
Ate1	A	T	7: 130,105,495 (GRCm39)	V298E	probably benign	Het
Atp6v1b2	A	G	8: 69,554,035 (GRCm39)	I71V	probably benign	Het
Bin1	A	G	18: 32,546,166 (GRCm39)	M112V	probably benign	Het
Camk2b	C	T	11: 5,940,383 (GRCm39)	A152T	probably benign	Het
Cars2	A	C	8: 11,579,706 (GRCm39)	F251V	probably damaging	Het
Cdkl1	A	T	12: 69,800,952 (GRCm39)	F229I	probably damaging	Het
Ceacam5	A	T	7: 17,486,171 (GRCm39)	Y556F	possibly damaging	Het
Chst15	T	C	7: 131,849,615 (GRCm39)	N442S	probably benign	Het
Ckap5	T	A	2: 91,436,707 (GRCm39)	D1602E	possibly damaging	Het
Cyp4f15	A	T	17: 32,909,733 (GRCm39)	D110V	possibly damaging	Het
Dlec1	A	G	9: 118,968,457 (GRCm39)	I1258V	probably benign	Het
Dpyd	A	G	3: 119,108,452 (GRCm39)	T832A	possibly damaging	Het
Eno1	A	G	4: 150,329,693 (GRCm39)	Y189C	probably damaging	Het
Gnat3	A	G	5: 18,208,838 (GRCm39)	T181A		Het
Kif1b	T	C	4: 149,306,805 (GRCm39)	M852V	probably damaging	Het
Klk1b26	A	T	7: 43,665,508 (GRCm39)	I139F	probably damaging	Het
Loxhd1	G	A	18: 77,493,681 (GRCm39)	V1547M	possibly damaging	Het
Lrp4	A	G	2: 91,318,790 (GRCm39)	T876A	probably damaging	Het
Malrd1	G	T	2: 15,638,035 (GRCm39)	W451L	unknown	Het
Marchf6	A	T	15: 31,494,262 (GRCm39)	N261K	possibly damaging	Het
Mcpt2	T	C	14: 56,280,250 (GRCm39)	C50R	probably damaging	Het
Muc16	A	G	9: 18,569,981 (GRCm39)	V846A	unknown	Het
Muc5b	A	T	7: 141,414,602 (GRCm39)	D2516V	unknown	Het
Myh15	T	C	16: 48,913,120 (GRCm39)	L359P	probably benign	Het
Nemp1	G	A	10: 127,528,898 (GRCm39)	V201I	probably benign	Het
Nr2e1	A	T	10: 42,444,425 (GRCm39)	L228Q	probably damaging	Het
Nrg1	C	A	8: 32,312,334 (GRCm39)	V388L	probably benign	Het
Nrg3	T	A	14: 38,734,053 (GRCm39)	T278S	probably damaging	Het
Numb	T	C	12: 83,854,990 (GRCm39)	E112G	probably benign	Het
Or1l4b	T	C	2: 37,036,778 (GRCm39)	S185P	probably damaging	Het
Or8g2b	A	C	9: 39,751,612 (GRCm39)	N294T	probably damaging	Het
Pdlim2	C	A	14: 70,403,563 (GRCm39)	C283F	probably damaging	Het
Potegl	T	A	2: 23,147,017 (GRCm39)		probably null	Het
Ppm1a	G	A	12: 72,830,909 (GRCm39)	G145R	probably damaging	Het
Pramel14	T	A	4: 143,720,809 (GRCm39)	D44V	probably benign	Het
Pramel18	A	T	4: 101,767,581 (GRCm39)	M277L	probably benign	Het
Prune2	C	A	19: 17,103,027 (GRCm39)	Q2729K	probably benign	Het
Repin1	G	T	6: 48,574,279 (GRCm39)	E403*	probably null	Het
Scn9a	G	T	2: 66,366,626 (GRCm39)	T719K	probably benign	Het
Slc12a7	T	C	13: 73,933,281 (GRCm39)	V113A	probably benign	Het
Slc23a1	C	T	18: 35,755,588 (GRCm39)	G436E	probably damaging	Het
Slc37a2	A	T	9: 37,149,510 (GRCm39)		probably null	Het
Steap1	G	A	5: 5,790,816 (GRCm39)	S44L	probably benign	Het
Sucnr1	C	T	3: 59,994,155 (GRCm39)	R228C	probably damaging	Het
Sult3a1	G	A	10: 33,742,517 (GRCm39)	G48D	probably damaging	Het
Syn3	A	T	10: 86,302,891 (GRCm39)	V88D	probably damaging	Het
Syne1	T	C	10: 5,058,622 (GRCm39)	D7297G	probably benign	Het
Tmco5	T	C	2: 116,710,734 (GRCm39)	I18T	probably damaging	Het
Trpc1	A	G	9: 95,608,601 (GRCm39)	L230P	probably damaging	Het
Ttn	T	C	2: 76,719,785 (GRCm39)	N7108S	unknown	Het
Ubr5	A	G	15: 38,025,081 (GRCm39)	V559A		Het
Ugt1a7c	T	C	1: 88,022,973 (GRCm39)	V44A	possibly damaging	Het
Vmn2r60	A	T	7: 41,790,494 (GRCm39)	S494C	possibly damaging	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
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'- GAATAGCCCAGATCGTGGTG -3'
(R):5'- TCTGCCACCCTGAGTCATAG -3'

Sequencing Primer
(F):5'- CCCAGATCGTGGTGGAGTG -3'
(R):5'- AGTCATAGGCGGCTCTCTGTC -3'

Posted On

2020-09-02