Mutagenetix > Incidental Mutations

Incidental Mutation 'R7177:Col9a1'

558655

Institutional Source

Beutler Lab

Gene Symbol

Col9a1

Ensembl Gene

ENSMUSG00000026147

Gene Name

collagen, type IX, alpha 1

Synonyms

Col9a-1

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.105) question?

Stock #

R7177 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

24177610-24252684 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 24195417 bp

Zygosity

Heterozygous

Amino Acid Change

Leucine to Glutamine at position 13 (L13Q)

Ref Sequence

ENSEMBL: ENSMUSP00000085687 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000054588] [ENSMUST00000088349]

Predicted Effect

probably benign
Transcript: ENSMUST00000054588

SMART Domains

Protein: ENSMUSP00000051579
Gene: ENSMUSG00000026147

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
TSPN	50	244	5.73e-78	SMART
Pfam:Collagen	266	326	2e-11	PFAM
Pfam:Collagen	308	358	3.5e-9	PFAM
Pfam:Collagen	357	409	1.2e-8	PFAM
Pfam:Collagen	415	472	7.8e-11	PFAM
Pfam:Collagen	454	515	2.9e-11	PFAM
Pfam:Collagen	592	667	3.9e-8	PFAM
Pfam:Collagen	646	716	1.7e-9	PFAM
Pfam:Collagen	697	760	1.6e-10	PFAM
Pfam:Collagen	785	848	3.1e-11	PFAM
low complexity region	878	899	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000088349
AA Change: L13Q

SMART Domains

Protein: ENSMUSP00000085687
Gene: ENSMUSG00000026147
AA Change: L13Q

Domain	Start	End	E-Value	Type
low complexity region	7	22	N/A	INTRINSIC
Pfam:Collagen	24	85	1.5e-11	PFAM
Pfam:Collagen	66	117	2.7e-9	PFAM
Pfam:Collagen	115	168	2.8e-8	PFAM
Pfam:Collagen	174	231	5.5e-11	PFAM
Pfam:Collagen	213	274	1.9e-11	PFAM
low complexity region	353	391	N/A	INTRINSIC
Pfam:Collagen	405	479	1.3e-9	PFAM
Pfam:Collagen	456	519	1e-10	PFAM
Pfam:Collagen	544	607	2.4e-11	PFAM
low complexity region	637	658	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 98.9%

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, which is a minor (5-20%) collagen component of hyaline cartilage. Type IX collagen is usually found in tissues containing type II collagen, a fibrillar collagen. Studies in knockout mice have shown that synthesis of the alpha 1 chain is essential for assembly of type IX collagen molecules, a heterotrimeric molecule, and that lack of type IX collagen is associated with early onset osteoarthritis. Mutations in this gene are associated with osteoarthritis in humans, with multiple epiphyseal dysplasia, 6, a form of chondrodysplasia, and with Stickler syndrome, a disease characterized by ophthalmic, orofacial, articular, and auditory defects. Two transcript variants that encode different isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygotes for a targeted mutation show no conspicuous skeletal abnormalities at birth but develop early-onset degenerative joint disease resembling osteoarthritis as well as progressive hearing loss; restoration and remodeling of trabecular bone is perturbed with minimal effects on cortical bone. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700029J07Rik	T	A	8: 45,970,407	E89D	possibly damaging	Het
4930550C14Rik	T	C	9: 53,414,385	L74S	probably damaging	Het
4933406M09Rik	T	C	1: 134,390,425	S312P	probably benign	Het
5730409E04Rik	A	G	4: 126,611,732	S18G	probably benign	Het
Adam29	A	G	8: 55,872,624	I265T	probably benign	Het
Aff4	C	T	11: 53,406,639	S896L	probably benign	Het
Ankrd27	T	C	7: 35,619,397	I571T	probably damaging	Het
Bdp1	C	A	13: 100,049,970	R1658I	probably damaging	Het
Carm1	C	T	9: 21,547,027	T7M	unknown	Het
Ccdc105	T	C	10: 78,752,490	D162G	probably damaging	Het
Ccdc183	A	G	2: 25,616,284	V100A	probably damaging	Het
Cd86	CA	CAA	16: 36,606,555		probably null	Het
Ceacam2	T	G	7: 25,520,916	D239A	probably benign	Het
Cmya5	T	C	13: 93,095,328	D1084G	probably benign	Het
Cog5	T	A	12: 31,760,889	I194K	probably damaging	Het
Col20a1	C	T	2: 180,994,214	Q211*	probably null	Het
Cracr2a	A	T	6: 127,608,706	M156L	probably benign	Het
Cts8	C	T	13: 61,251,691	M151I	possibly damaging	Het
Cyp2ab1	A	T	16: 20,316,719	L11Q	probably null	Het
Dhrs13	T	A	11: 78,034,382	C160S	probably benign	Het
Enthd1	T	A	15: 80,474,214	E368D	probably damaging	Het
Fbxo18	A	G	2: 11,755,711	I676T	probably damaging	Het
Fcgrt	T	C	7: 45,101,997	R176G	probably benign	Het
Gatd1	A	G	7: 141,411,034	F67L	possibly damaging	Het
Gm4353	G	A	7: 116,084,492	P23S	probably damaging	Het
Gm6882	T	A	7: 21,427,752	I64F	possibly damaging	Het
Grwd1	A	T	7: 45,830,780	M1K	probably null	Het
Hook2	T	A	8: 84,991,417	S58T	probably benign	Het
Iqch	T	G	9: 63,421,835	*1072C	probably null	Het
Kmt2d	G	A	15: 98,850,386	T3019I	unknown	Het
Lmx1a	T	C	1: 167,846,678	S356P	probably benign	Het
Lrig3	A	G	10: 126,006,843	M546V	probably benign	Het
Lrrc1	C	A	9: 77,472,222	E96*	probably null	Het
Lrtm2	C	A	6: 119,317,152	M339I	probably damaging	Het
Map10	T	C	8: 125,671,845	V659A	probably benign	Het
Map7d1	A	G	4: 126,236,985	C384R	probably damaging	Het
Mcur1	T	C	13: 43,544,536	D296G	probably damaging	Het
Mettl24	A	T	10: 40,810,512	H295L	probably damaging	Het
Mpl	A	G	4: 118,448,544		probably null	Het
Mrps5	T	C	2: 127,595,697	V148A	probably benign	Het
N4bp2	T	C	5: 65,807,548	V980A	probably damaging	Het
Ncaph	A	T	2: 127,116,586	D504E	probably damaging	Het
Nxph1	A	G	6: 9,247,497	N156S	probably damaging	Het
Odf3l1	T	A	9: 56,849,978	M139L	possibly damaging	Het
Olfr1307	T	A	2: 111,945,156	Q100L	probably damaging	Het
Olfr1395	T	A	11: 49,149,185	C309*	probably null	Het
Pafah1b3	T	A	7: 25,295,232	I186L	probably benign	Het
Papola	C	A	12: 105,809,531	N235K	possibly damaging	Het
Pcnx3	A	T	19: 5,687,499	M98K	probably benign	Het
Pkhd1l1	A	G	15: 44,467,404	N125S	probably damaging	Het
Pls1	T	A	9: 95,773,559	H380L	probably benign	Het
Plxna1	T	C	6: 89,323,329	T1591A	possibly damaging	Het
Pparg	T	G	6: 115,441,620	S147A	probably benign	Het
Prdm10	T	C	9: 31,367,707	S1025P	probably benign	Het
Prkcd	T	A	14: 30,599,707	H510L	probably damaging	Het
Ptprh	T	A	7: 4,569,481	E499D	possibly damaging	Het
Rad51ap1	A	G	6: 126,925,020	S256P	probably benign	Het
Rad54b	A	G	4: 11,599,755	T320A	probably damaging	Het
Rnf207	A	G	4: 152,312,177	I459T	probably benign	Het
Runx2	G	A	17: 44,814,192	P80L	probably damaging	Het
Ryr3	A	T	2: 112,900,843	D727E	probably damaging	Het
Sdk2	C	T	11: 113,829,969	R1378H	possibly damaging	Het
Slc7a11	A	G	3: 50,443,231	S11P	probably benign	Het
Sox4	A	G	13: 28,953,017	V2A	probably damaging	Het
Srf	A	G	17: 46,555,392	F146S	probably damaging	Het
Srrm2	T	C	17: 23,816,773	V797A	unknown	Het
Stk32c	T	C	7: 139,104,302	D463G	possibly damaging	Het
Syne2	C	A	12: 75,971,880	Y3384*	probably null	Het
Tmem55b	A	C	14: 50,930,177	M104R	possibly damaging	Het
Traip	T	A	9: 107,960,985	M139K	possibly damaging	Het
Trappc2l	T	A	8: 122,614,312	F100Y	probably damaging	Het
Ush1c	T	C	7: 46,229,219	D124G	probably damaging	Het
Uty	A	G	Y: 1,099,691	V1168A	probably benign	Het
Vmn2r25	T	C	6: 123,839,923	D233G	possibly damaging	Het
Zdbf2	C	T	1: 63,294,961	R31C	possibly damaging	Het

Other mutations in Col9a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00233:Col9a1	APN	1	24185225	missense	unknown
IGL00517:Col9a1	APN	1	24195534	intron	probably benign
IGL01125:Col9a1	APN	1	24224645	critical splice acceptor site	probably null
IGL01505:Col9a1	APN	1	24185124	missense	unknown
IGL01583:Col9a1	APN	1	24185144	missense	unknown
IGL01627:Col9a1	APN	1	24179608	critical splice donor site	probably null
IGL01773:Col9a1	APN	1	24205066	missense	probably benign	0.17
IGL02117:Col9a1	APN	1	24237493	nonsense	probably null
IGL02192:Col9a1	APN	1	24221987	missense	probably damaging	1.00
IGL02346:Col9a1	APN	1	24223609	missense	probably damaging	0.96
IGL02383:Col9a1	APN	1	24185258	missense	unknown
IGL02453:Col9a1	APN	1	24179357	missense	unknown
IGL02553:Col9a1	APN	1	24221937	splice site	probably benign
IGL03412:Col9a1	APN	1	24210427	critical splice donor site	probably null
IGL03493:Col9a1	APN	1	24221570	splice site	probably benign
ANU74:Col9a1	UTSW	1	24185328	missense	unknown
R0076:Col9a1	UTSW	1	24237497	critical splice donor site	probably null
R0076:Col9a1	UTSW	1	24237497	critical splice donor site	probably null
R0090:Col9a1	UTSW	1	24223562	splice site	probably null
R0356:Col9a1	UTSW	1	24185247	nonsense	probably null
R0562:Col9a1	UTSW	1	24179279	splice site	probably null
R0584:Col9a1	UTSW	1	24224490	splice site	probably benign
R0708:Col9a1	UTSW	1	24237261	missense	possibly damaging	0.92
R1342:Col9a1	UTSW	1	24223620	critical splice donor site	probably null
R1445:Col9a1	UTSW	1	24237498	critical splice donor site	probably null
R1791:Col9a1	UTSW	1	24185305	missense	unknown
R1938:Col9a1	UTSW	1	24222473	missense	probably damaging	1.00
R2214:Col9a1	UTSW	1	24208202	missense	probably damaging	1.00
R2240:Col9a1	UTSW	1	24179501	missense	unknown
R3757:Col9a1	UTSW	1	24232231	critical splice donor site	probably null
R3891:Col9a1	UTSW	1	24185436	critical splice donor site	probably null
R4249:Col9a1	UTSW	1	24244381	missense	probably damaging	1.00
R4690:Col9a1	UTSW	1	24224706	splice site	probably null
R4918:Col9a1	UTSW	1	24237258	missense	possibly damaging	0.74
R4988:Col9a1	UTSW	1	24185192	missense	unknown
R5144:Col9a1	UTSW	1	24239353	missense	probably benign	0.08
R5327:Col9a1	UTSW	1	24195539	critical splice donor site	probably null
R5511:Col9a1	UTSW	1	24179538	missense	unknown
R5519:Col9a1	UTSW	1	24230254	splice site	probably null
R5564:Col9a1	UTSW	1	24195355	start gained	probably benign
R6076:Col9a1	UTSW	1	24195376	start gained	probably benign
R6478:Col9a1	UTSW	1	24185405	missense	unknown
R6886:Col9a1	UTSW	1	24185345	missense	unknown
R7259:Col9a1	UTSW	1	24185343	missense	unknown
R7268:Col9a1	UTSW	1	24207398	missense	possibly damaging	0.89
R7347:Col9a1	UTSW	1	24179403	splice site	probably null
R7644:Col9a1	UTSW	1	24185162	missense	unknown
R7860:Col9a1	UTSW	1	24237180	missense	probably damaging	1.00
R8267:Col9a1	UTSW	1	24185186	missense	unknown
R8296:Col9a1	UTSW	1	24178299	missense	unknown
Z1176:Col9a1	UTSW	1	24214588	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- AAGAAACCCAGGTCCCCTTG -3'
(R):5'- GGGTACTCTGACTTCTCACACC -3'

Sequencing Primer
(F):5'- TTGGCCAGGCACCTTTG -3'
(R):5'- GTACTCTGACTTCTCACACCCAGAAC -3'

Posted On

2019-06-26