Mutagenetix > Incidental Mutations

Incidental Mutation 'R5566:Col20a1'

436790

Institutional Source

Beutler Lab

Gene Symbol

Col20a1

Ensembl Gene

ENSMUSG00000016356

Gene Name

collagen, type XX, alpha 1

Synonyms

1700051I12Rik

MMRRC Submission

043123-MU

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5566 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

180986535-181018363 bp(+) (GRCm38)

Type of Mutation

splice site

DNA Base Change (assembly)

A to T at 180986523 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000153871 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000029092] [ENSMUST00000108856] [ENSMUST00000108859] [ENSMUST00000108860] [ENSMUST00000108861] [ENSMUST00000108862] [ENSMUST00000149179] [ENSMUST00000228434]

AlphaFold

Q923P0

Predicted Effect

probably benign
Transcript: ENSMUST00000029092

SMART Domains

Protein: ENSMUSP00000029092
Gene: ENSMUSG00000027575

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	310	327	N/A	INTRINSIC
low complexity region	334	347	N/A	INTRINSIC
low complexity region	359	392	N/A	INTRINSIC
low complexity region	394	401	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000094214

SMART Domains

Protein: ENSMUSP00000091767
Gene: ENSMUSG00000070461

Domain	Start	End	E-Value	Type
low complexity region	107	120	N/A	INTRINSIC

Predicted Effect

probably null
Transcript: ENSMUST00000108856

SMART Domains

Protein: ENSMUSP00000104484
Gene: ENSMUSG00000016356

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
FN3	24	103	2.18e1	SMART
VWA	175	354	4.68e-55	SMART
FN3	375	453	6.2e-7	SMART
FN3	464	543	7.34e-9	SMART
FN3	555	633	8.18e-7	SMART
FN3	644	723	8.98e-4	SMART
FN3	738	817	1.43e-11	SMART
TSPN	840	1035	6.45e-31	SMART
Pfam:Collagen	1067	1125	3.8e-9	PFAM
Pfam:Collagen	1122	1174	7.4e-9	PFAM
Pfam:Collagen	1165	1223	3e-11	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108859

SMART Domains

Protein: ENSMUSP00000104487
Gene: ENSMUSG00000027575

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	288	305	N/A	INTRINSIC
low complexity region	312	325	N/A	INTRINSIC
low complexity region	337	370	N/A	INTRINSIC
low complexity region	372	379	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108860

SMART Domains

Protein: ENSMUSP00000104488
Gene: ENSMUSG00000027575

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	288	305	N/A	INTRINSIC
low complexity region	312	325	N/A	INTRINSIC
low complexity region	337	370	N/A	INTRINSIC
low complexity region	372	379	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108861

SMART Domains

Protein: ENSMUSP00000104489
Gene: ENSMUSG00000027575

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	290	307	N/A	INTRINSIC
low complexity region	314	327	N/A	INTRINSIC
low complexity region	339	372	N/A	INTRINSIC
low complexity region	374	381	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000108862

SMART Domains

Protein: ENSMUSP00000104490
Gene: ENSMUSG00000027575

Domain	Start	End	E-Value	Type
ArfGap	7	124	2.4e-54	SMART
low complexity region	149	160	N/A	INTRINSIC
PDB:2M0W\|A	198	220	1e-6	PDB
low complexity region	290	307	N/A	INTRINSIC
low complexity region	314	327	N/A	INTRINSIC
low complexity region	339	372	N/A	INTRINSIC
low complexity region	374	381	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136590

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000145629

Predicted Effect

probably null
Transcript: ENSMUST00000149179

SMART Domains

Protein: ENSMUSP00000115291
Gene: ENSMUSG00000016356

Domain	Start	End	E-Value	Type
signal peptide	1	23	N/A	INTRINSIC
FN3	24	103	2.18e1	SMART
VWA	175	354	4.68e-55	SMART
FN3	375	453	6.2e-7	SMART
FN3	464	543	7.34e-9	SMART
FN3	555	633	8.18e-7	SMART
FN3	644	723	8.98e-4	SMART
FN3	738	817	1.43e-11	SMART
TSPN	840	1035	6.45e-31	SMART
low complexity region	1069	1106	N/A	INTRINSIC
low complexity region	1108	1121	N/A	INTRINSIC
low complexity region	1136	1155	N/A	INTRINSIC
Blast:TSPN	1156	1202	2e-19	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000189441

Predicted Effect

probably null
Transcript: ENSMUST00000228434

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.4%
20x: 95.5%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 97 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
3110002H16Rik	T	C	18: 12,180,692	I26T	possibly damaging	Het
Abca13	T	A	11: 9,294,615	Y2159*	probably null	Het
Abca3	A	G	17: 24,383,927	T499A	probably benign	Het
Abcb5	T	A	12: 118,935,967	T322S	probably damaging	Het
Adamts4	T	A	1: 171,250,850	M1K	probably null	Het
Adamtsl4	C	T	3: 95,685,455		probably null	Het
Adh4	A	T	3: 138,424,189	I259F	probably damaging	Het
Aff3	G	A	1: 38,181,424	S1135F	probably damaging	Het
Arhgef16	T	C	4: 154,285,648	D280G	probably benign	Het
Baiap3	T	C	17: 25,251,733	E71G	probably damaging	Het
BC030867	T	A	11: 102,255,833	S312T	probably damaging	Het
Calb2	A	G	8: 110,152,700	I91T	possibly damaging	Het
Ccr5	A	G	9: 124,124,660	N100S	probably benign	Het
Cep57	G	T	9: 13,821,575	R25S	probably damaging	Het
Chadl	A	G	15: 81,695,878	L52P	probably damaging	Het
Clec12b	T	C	6: 129,385,475	T6A	probably damaging	Het
Cnga1	T	A	5: 72,618,250	N43Y	probably damaging	Het
Csmd2	T	C	4: 128,462,889		probably null	Het
Ctps	A	T	4: 120,554,103		probably null	Het
Cyp39a1	T	A	17: 43,685,208	W224R	possibly damaging	Het
Defb29	A	T	2: 152,538,928	Y54N	probably benign	Het
Dmbt1	A	T	7: 131,106,273	D1241V	probably damaging	Het
Dnah1	A	T	14: 31,274,366	I2671K	probably benign	Het
Dnah2	C	A	11: 69,516,569	E158*	probably null	Het
Edar	A	G	10: 58,628,641	S59P	possibly damaging	Het
Egr2	T	A	10: 67,540,766	C339*	probably null	Het
Eif5b	G	A	1: 38,045,684	V871I	possibly damaging	Het
Eif5b	G	A	1: 38,051,247	G1169E	probably damaging	Het
Erap1	A	G	13: 74,662,412	Y290C	probably damaging	Het
Fastkd5	T	A	2: 130,614,301	T790S	possibly damaging	Het
Fkrp	C	T	7: 16,810,924	V338M	probably damaging	Het
Gabra6	T	C	11: 42,307,490	T378A	probably benign	Het
Gm4924	C	A	10: 82,378,641	Q17K	possibly damaging	Het
Gm9847	A	G	12: 14,494,999		noncoding transcript	Het
Gpr108	A	G	17: 57,236,919	F429S	probably damaging	Het
Gpr162	G	A	6: 124,860,938	R250*	probably null	Het
Gtf2a1	A	T	12: 91,567,594	D295E	possibly damaging	Het
Gtf2h3	C	T	5: 124,584,297	T121I	probably benign	Het
Herc1	T	A	9: 66,465,537	M3125K	possibly damaging	Het
Hoxb6	T	A	11: 96,300,754	Y167*	probably null	Het
Htt	T	C	5: 34,849,075	Y1443H	probably damaging	Het
Il21r	A	G	7: 125,625,298	D28G	probably damaging	Het
Impact	T	G	18: 12,974,762	V29G	probably damaging	Het
Itpr3	A	G	17: 27,115,952	T2147A	possibly damaging	Het
Itsn2	T	A	12: 4,626,554	L50Q	probably damaging	Het
Jade1	A	G	3: 41,604,903	D473G	possibly damaging	Het
Kif26a	T	G	12: 112,157,354	L131R	probably damaging	Het
Kif2a	A	T	13: 106,993,924	M1K	probably null	Het
Lrsam1	C	A	2: 32,941,858	Q368H	probably damaging	Het
Macf1	T	C	4: 123,435,164	Q4592R	probably damaging	Het
Map3k5	T	C	10: 20,110,719	V893A	probably damaging	Het
Med13l	G	T	5: 118,728,665	V595F	possibly damaging	Het
Mocs1	T	A	17: 49,454,183	L435Q	possibly damaging	Het
Mtmr4	T	C	11: 87,604,530	L471P	probably damaging	Het
Myo7a	T	C	7: 98,064,816	E1616G	possibly damaging	Het
Nacad	T	A	11: 6,602,136	S352C	probably damaging	Het
Nfat5	T	A	8: 107,369,135	M817K	possibly damaging	Het
Ofcc1	C	A	13: 40,094,653	L668F	probably damaging	Het
Olfr1062	G	A	2: 86,423,377	Q100*	probably null	Het
Olfr18	T	C	9: 20,313,969	Q309R	probably benign	Het
Olfr527	C	A	7: 140,336,067	D68E	probably damaging	Het
Plxnb2	T	C	15: 89,164,020	T696A	probably benign	Het
Prkab2	T	A	3: 97,662,293	F58L	probably benign	Het
Prpf4	G	T	4: 62,415,969	L220F	probably benign	Het
Rad18	A	T	6: 112,681,346	D199E	probably benign	Het
Raet1e	T	C	10: 22,174,405	L29P	probably damaging	Het
Ralgapb	A	C	2: 158,494,710	T1089P	possibly damaging	Het
Rest	A	G	5: 77,282,326	E864G	probably benign	Het
Rgsl1	T	A	1: 153,793,774	I289F	probably damaging	Het
Rint1	T	C	5: 23,810,953	Y406H	probably damaging	Het
Rpl31	C	T	1: 39,370,027	R41C	probably benign	Het
Scn8a	T	C	15: 100,974,534	S485P	probably damaging	Het
Slamf1	T	A	1: 171,787,970	V249E	possibly damaging	Het
Slc39a12	C	T	2: 14,407,603	T362I	possibly damaging	Het
Sos1	C	T	17: 80,453,890	V126I	possibly damaging	Het
Srcap	T	C	7: 127,525,303	F215S	probably damaging	Het
Supt4a	T	A	11: 87,743,287	S110T	probably benign	Het
Tbc1d30	T	A	10: 121,302,110	T232S	probably damaging	Het
Tctex1d2	A	G	16: 32,419,900	Y31C	probably damaging	Het
Tenm3	A	G	8: 48,279,006	C1288R	probably damaging	Het
Tespa1	T	A	10: 130,355,487	L100*	probably null	Het
Tgm1	C	A	14: 55,712,436	R105L	probably damaging	Het
Tgoln1	G	A	6: 72,616,035	T154I	possibly damaging	Het
Trp53i13	G	A	11: 77,508,726	T259I	probably damaging	Het
Tubgcp4	T	A	2: 121,184,770	F320I	possibly damaging	Het
Vmn1r21	A	C	6: 57,844,094	Y122D	probably benign	Het
Vmn1r75	T	A	7: 11,880,480	D46E	probably damaging	Het
Vmn2r120	A	T	17: 57,545,290	L9M	possibly damaging	Het
Vmn2r59	A	G	7: 42,046,823	I165T	possibly damaging	Het
Vmn2r76	A	T	7: 86,226,078	Y564N	probably damaging	Het
Wee1	G	T	7: 110,126,050	E300*	probably null	Het
Xdh	T	C	17: 73,893,622	D1168G	probably damaging	Het
Zcchc6	A	T	13: 59,788,629	C817*	probably null	Het
Zfp54	A	G	17: 21,433,444	T67A	probably damaging	Het
Zfp941	G	T	7: 140,812,766	H227N	probably benign	Het
Zpr1	T	A	9: 46,281,075	V399D	possibly damaging	Het
Zzz3	A	G	3: 152,455,824	E285G	probably damaging	Het

Other mutations in Col20a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00781:Col20a1	APN	2	181003479	missense	possibly damaging	0.93
IGL00975:Col20a1	APN	2	180992478	missense	probably damaging	1.00
IGL01094:Col20a1	APN	2	180999766	missense	probably damaging	0.99
IGL01388:Col20a1	APN	2	181003471	missense	probably benign	0.24
IGL01472:Col20a1	APN	2	181007832	missense	probably benign	0.44
IGL01936:Col20a1	APN	2	181009368	splice site	probably benign
IGL02133:Col20a1	APN	2	181007144	missense	probably damaging	1.00
IGL02318:Col20a1	APN	2	181007159	missense	probably damaging	0.99
IGL02576:Col20a1	APN	2	181013405	nonsense	probably null
IGL02822:Col20a1	APN	2	180996807	missense	probably damaging	1.00
IGL02898:Col20a1	APN	2	180989112	nonsense	probably null
IGL03056:Col20a1	APN	2	180994889	missense	probably damaging	1.00
IGL03189:Col20a1	APN	2	181009407	nonsense	probably null
IGL03196:Col20a1	APN	2	181007878	splice site	probably null
R0001:Col20a1	UTSW	2	180984412	unclassified	probably benign
R0200:Col20a1	UTSW	2	181000438	missense	probably damaging	1.00
R0384:Col20a1	UTSW	2	180999162	missense	probably benign	0.00
R0964:Col20a1	UTSW	2	180984485	unclassified	probably benign
R0975:Col20a1	UTSW	2	181006826	missense	possibly damaging	0.75
R1359:Col20a1	UTSW	2	180999792	missense	probably benign	0.02
R1395:Col20a1	UTSW	2	180998607	missense	probably damaging	0.99
R1470:Col20a1	UTSW	2	180994960	missense	probably benign	0.01
R1470:Col20a1	UTSW	2	180994960	missense	probably benign	0.01
R1508:Col20a1	UTSW	2	180992577	missense	probably damaging	0.98
R1865:Col20a1	UTSW	2	181015813	missense	possibly damaging	0.87
R1883:Col20a1	UTSW	2	180992910	missense	possibly damaging	0.52
R1884:Col20a1	UTSW	2	180992910	missense	possibly damaging	0.52
R1906:Col20a1	UTSW	2	180998697	missense	probably benign	0.00
R2020:Col20a1	UTSW	2	181013163	critical splice donor site	probably null
R2121:Col20a1	UTSW	2	180996456	missense	probably damaging	0.99
R2131:Col20a1	UTSW	2	180992573	missense	probably damaging	1.00
R2343:Col20a1	UTSW	2	181001331	missense	possibly damaging	0.73
R3153:Col20a1	UTSW	2	181008593	missense	probably damaging	1.00
R3430:Col20a1	UTSW	2	181013285	nonsense	probably null
R3547:Col20a1	UTSW	2	180994911	missense	probably damaging	1.00
R3844:Col20a1	UTSW	2	180992449	missense	probably damaging	1.00
R3914:Col20a1	UTSW	2	180998492	missense	probably benign	0.00
R4414:Col20a1	UTSW	2	181001250	missense	possibly damaging	0.92
R4711:Col20a1	UTSW	2	180992491	missense	probably damaging	1.00
R4760:Col20a1	UTSW	2	180984403	unclassified	probably benign
R4771:Col20a1	UTSW	2	180989124	missense	probably benign	0.17
R4809:Col20a1	UTSW	2	180998661	missense	probably damaging	1.00
R4872:Col20a1	UTSW	2	180997363	missense	possibly damaging	0.74
R5045:Col20a1	UTSW	2	181006845	missense	probably damaging	1.00
R5238:Col20a1	UTSW	2	180998586	missense	probably damaging	1.00
R6389:Col20a1	UTSW	2	180992583	splice site	probably null
R6422:Col20a1	UTSW	2	181014819	missense	possibly damaging	0.75
R6924:Col20a1	UTSW	2	180996850	missense	probably damaging	1.00
R6982:Col20a1	UTSW	2	180996706	missense	probably benign	0.00
R7177:Col20a1	UTSW	2	180994214	nonsense	probably null
R7195:Col20a1	UTSW	2	181007231	missense	probably damaging	1.00
R7717:Col20a1	UTSW	2	181007615	missense	probably damaging	1.00
R7872:Col20a1	UTSW	2	180986578	missense	probably benign	0.14
R8183:Col20a1	UTSW	2	180998414	missense
R8188:Col20a1	UTSW	2	181016333	critical splice donor site	probably null
R8331:Col20a1	UTSW	2	180996766	missense	possibly damaging	0.95
R8423:Col20a1	UTSW	2	180998705	missense	probably damaging	1.00
R8803:Col20a1	UTSW	2	181001338	missense	possibly damaging	0.75
R8849:Col20a1	UTSW	2	180998639	missense	probably damaging	1.00
R8855:Col20a1	UTSW	2	181013891	missense
R8885:Col20a1	UTSW	2	180998503	splice site	probably benign
R9160:Col20a1	UTSW	2	180999745	missense	probably benign
R9223:Col20a1	UTSW	2	181006735	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGATGCCTTAGTATGGCTTCAG -3'
(R):5'- CAGCTTGCCTGTTGCTAGAAC -3'

Sequencing Primer
(F):5'- AGTATGGCTTCAGTCTTCATCAAC -3'
(R):5'- CTCAGGCTGGCATTTACTACAGG -3'

Posted On

2016-10-24