Mutagenetix > Incidental Mutation

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

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R5566 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

180628328-180660156 bp(+) (GRCm39)

Type of Mutation

splice site

DNA Base Change (assembly)

A to T at 180628316 bp (GRCm39)

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: ENSMUST00000189441

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: ENSMUST00000145629

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136590

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
Abca13	T	A	11: 9,244,615 (GRCm39)	Y2159*	probably null	Het
Abca3	A	G	17: 24,602,901 (GRCm39)	T499A	probably benign	Het
Abcb5	T	A	12: 118,899,702 (GRCm39)	T322S	probably damaging	Het
Adamts4	T	A	1: 171,078,419 (GRCm39)	M1K	probably null	Het
Adamtsl4	C	T	3: 95,592,765 (GRCm39)		probably null	Het
Adh4	A	T	3: 138,129,950 (GRCm39)	I259F	probably damaging	Het
Aff3	G	A	1: 38,220,505 (GRCm39)	S1135F	probably damaging	Het
Arhgef16	T	C	4: 154,370,105 (GRCm39)	D280G	probably benign	Het
Baiap3	T	C	17: 25,470,707 (GRCm39)	E71G	probably damaging	Het
Calb2	A	G	8: 110,879,332 (GRCm39)	I91T	possibly damaging	Het
Ccr5	A	G	9: 123,924,697 (GRCm39)	N100S	probably benign	Het
Cep57	G	T	9: 13,732,871 (GRCm39)	R25S	probably damaging	Het
Chadl	A	G	15: 81,580,079 (GRCm39)	L52P	probably damaging	Het
Clec12b	T	C	6: 129,362,438 (GRCm39)	T6A	probably damaging	Het
Cnga1	T	A	5: 72,775,593 (GRCm39)	N43Y	probably damaging	Het
Csmd2	T	C	4: 128,356,682 (GRCm39)		probably null	Het
Ctps1	A	T	4: 120,411,300 (GRCm39)		probably null	Het
Cyp39a1	T	A	17: 43,996,099 (GRCm39)	W224R	possibly damaging	Het
Defb29	A	T	2: 152,380,848 (GRCm39)	Y54N	probably benign	Het
Dmbt1	A	T	7: 130,708,003 (GRCm39)	D1241V	probably damaging	Het
Dnah1	A	T	14: 30,996,323 (GRCm39)	I2671K	probably benign	Het
Dnah2	C	A	11: 69,407,395 (GRCm39)	E158*	probably null	Het
Dynlt2b	A	G	16: 32,238,718 (GRCm39)	Y31C	probably damaging	Het
Edar	A	G	10: 58,464,463 (GRCm39)	S59P	possibly damaging	Het
Egr2	T	A	10: 67,376,596 (GRCm39)	C339*	probably null	Het
Eif5b	G	A	1: 38,084,765 (GRCm39)	V871I	possibly damaging	Het
Eif5b	G	A	1: 38,090,328 (GRCm39)	G1169E	probably damaging	Het
Erap1	A	G	13: 74,810,531 (GRCm39)	Y290C	probably damaging	Het
Fastkd5	T	A	2: 130,456,221 (GRCm39)	T790S	possibly damaging	Het
Fkrp	C	T	7: 16,544,849 (GRCm39)	V338M	probably damaging	Het
Gabra6	T	C	11: 42,198,317 (GRCm39)	T378A	probably benign	Het
Gm4924	C	A	10: 82,214,475 (GRCm39)	Q17K	possibly damaging	Het
Gm9847	A	G	12: 14,545,000 (GRCm39)		noncoding transcript	Het
Gpr108	A	G	17: 57,543,919 (GRCm39)	F429S	probably damaging	Het
Gpr162	G	A	6: 124,837,901 (GRCm39)	R250*	probably null	Het
Gtf2a1	A	T	12: 91,534,368 (GRCm39)	D295E	possibly damaging	Het
Gtf2h3	C	T	5: 124,722,360 (GRCm39)	T121I	probably benign	Het
Herc1	T	A	9: 66,372,819 (GRCm39)	M3125K	possibly damaging	Het
Hoxb6	T	A	11: 96,191,580 (GRCm39)	Y167*	probably null	Het
Hrob	T	A	11: 102,146,659 (GRCm39)	S312T	probably damaging	Het
Htt	T	C	5: 35,006,419 (GRCm39)	Y1443H	probably damaging	Het
Il21r	A	G	7: 125,224,470 (GRCm39)	D28G	probably damaging	Het
Impact	T	G	18: 13,107,819 (GRCm39)	V29G	probably damaging	Het
Itpr3	A	G	17: 27,334,926 (GRCm39)	T2147A	possibly damaging	Het
Itsn2	T	A	12: 4,676,554 (GRCm39)	L50Q	probably damaging	Het
Jade1	A	G	3: 41,559,338 (GRCm39)	D473G	possibly damaging	Het
Kif26a	T	G	12: 112,123,788 (GRCm39)	L131R	probably damaging	Het
Kif2a	A	T	13: 107,130,432 (GRCm39)	M1K	probably null	Het
Lrsam1	C	A	2: 32,831,870 (GRCm39)	Q368H	probably damaging	Het
Macf1	T	C	4: 123,328,957 (GRCm39)	Q4592R	probably damaging	Het
Map3k5	T	C	10: 19,986,465 (GRCm39)	V893A	probably damaging	Het
Med13l	G	T	5: 118,866,730 (GRCm39)	V595F	possibly damaging	Het
Mocs1	T	A	17: 49,761,211 (GRCm39)	L435Q	possibly damaging	Het
Mtmr4	T	C	11: 87,495,356 (GRCm39)	L471P	probably damaging	Het
Myo7a	T	C	7: 97,714,023 (GRCm39)	E1616G	possibly damaging	Het
Nacad	T	A	11: 6,552,136 (GRCm39)	S352C	probably damaging	Het
Nfat5	T	A	8: 108,095,767 (GRCm39)	M817K	possibly damaging	Het
Ofcc1	C	A	13: 40,248,129 (GRCm39)	L668F	probably damaging	Het
Or12j2	C	A	7: 139,915,980 (GRCm39)	D68E	probably damaging	Het
Or7e178	T	C	9: 20,225,265 (GRCm39)	Q309R	probably benign	Het
Or8j3c	G	A	2: 86,253,721 (GRCm39)	Q100*	probably null	Het
Plxnb2	T	C	15: 89,048,223 (GRCm39)	T696A	probably benign	Het
Prkab2	T	A	3: 97,569,609 (GRCm39)	F58L	probably benign	Het
Prpf4	G	T	4: 62,334,206 (GRCm39)	L220F	probably benign	Het
Rad18	A	T	6: 112,658,307 (GRCm39)	D199E	probably benign	Het
Raet1e	T	C	10: 22,050,304 (GRCm39)	L29P	probably damaging	Het
Ralgapb	A	C	2: 158,336,630 (GRCm39)	T1089P	possibly damaging	Het
Rest	A	G	5: 77,430,173 (GRCm39)	E864G	probably benign	Het
Rgsl1	T	A	1: 153,669,520 (GRCm39)	I289F	probably damaging	Het
Rint1	T	C	5: 24,015,951 (GRCm39)	Y406H	probably damaging	Het
Rmc1	T	C	18: 12,313,749 (GRCm39)	I26T	possibly damaging	Het
Rpl31	C	T	1: 39,409,108 (GRCm39)	R41C	probably benign	Het
Scn8a	T	C	15: 100,872,415 (GRCm39)	S485P	probably damaging	Het
Slamf1	T	A	1: 171,615,538 (GRCm39)	V249E	possibly damaging	Het
Slc39a12	C	T	2: 14,412,414 (GRCm39)	T362I	possibly damaging	Het
Sos1	C	T	17: 80,761,319 (GRCm39)	V126I	possibly damaging	Het
Srcap	T	C	7: 127,124,475 (GRCm39)	F215S	probably damaging	Het
Supt4a	T	A	11: 87,634,113 (GRCm39)	S110T	probably benign	Het
Tbc1d30	T	A	10: 121,138,015 (GRCm39)	T232S	probably damaging	Het
Tenm3	A	G	8: 48,732,041 (GRCm39)	C1288R	probably damaging	Het
Tespa1	T	A	10: 130,191,356 (GRCm39)	L100*	probably null	Het
Tgm1	C	A	14: 55,949,893 (GRCm39)	R105L	probably damaging	Het
Tgoln1	G	A	6: 72,593,018 (GRCm39)	T154I	possibly damaging	Het
Trp53i13	G	A	11: 77,399,552 (GRCm39)	T259I	probably damaging	Het
Tubgcp4	T	A	2: 121,015,251 (GRCm39)	F320I	possibly damaging	Het
Tut7	A	T	13: 59,936,443 (GRCm39)	C817*	probably null	Het
Vmn1r21	A	C	6: 57,821,079 (GRCm39)	Y122D	probably benign	Het
Vmn1r75	T	A	7: 11,614,407 (GRCm39)	D46E	probably damaging	Het
Vmn2r120	A	T	17: 57,852,290 (GRCm39)	L9M	possibly damaging	Het
Vmn2r59	A	G	7: 41,696,247 (GRCm39)	I165T	possibly damaging	Het
Vmn2r76	A	T	7: 85,875,286 (GRCm39)	Y564N	probably damaging	Het
Wee1	G	T	7: 109,725,257 (GRCm39)	E300*	probably null	Het
Xdh	T	C	17: 74,200,617 (GRCm39)	D1168G	probably damaging	Het
Zfp54	A	G	17: 21,653,706 (GRCm39)	T67A	probably damaging	Het
Zfp941	G	T	7: 140,392,679 (GRCm39)	H227N	probably benign	Het
Zpr1	T	A	9: 46,192,373 (GRCm39)	V399D	possibly damaging	Het
Zzz3	A	G	3: 152,161,461 (GRCm39)	E285G	probably damaging	Het

Other mutations in Col20a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00781:Col20a1	APN	2	180,645,272 (GRCm39)	missense	possibly damaging	0.93
IGL00975:Col20a1	APN	2	180,634,271 (GRCm39)	missense	probably damaging	1.00
IGL01094:Col20a1	APN	2	180,641,559 (GRCm39)	missense	probably damaging	0.99
IGL01388:Col20a1	APN	2	180,645,264 (GRCm39)	missense	probably benign	0.24
IGL01472:Col20a1	APN	2	180,649,625 (GRCm39)	missense	probably benign	0.44
IGL01936:Col20a1	APN	2	180,651,161 (GRCm39)	splice site	probably benign
IGL02133:Col20a1	APN	2	180,648,937 (GRCm39)	missense	probably damaging	1.00
IGL02318:Col20a1	APN	2	180,648,952 (GRCm39)	missense	probably damaging	0.99
IGL02576:Col20a1	APN	2	180,655,198 (GRCm39)	nonsense	probably null
IGL02822:Col20a1	APN	2	180,638,600 (GRCm39)	missense	probably damaging	1.00
IGL02898:Col20a1	APN	2	180,630,905 (GRCm39)	nonsense	probably null
IGL03056:Col20a1	APN	2	180,636,682 (GRCm39)	missense	probably damaging	1.00
IGL03189:Col20a1	APN	2	180,651,200 (GRCm39)	nonsense	probably null
IGL03196:Col20a1	APN	2	180,649,671 (GRCm39)	splice site	probably null
R0001:Col20a1	UTSW	2	180,626,205 (GRCm39)	unclassified	probably benign
R0200:Col20a1	UTSW	2	180,642,231 (GRCm39)	missense	probably damaging	1.00
R0384:Col20a1	UTSW	2	180,640,955 (GRCm39)	missense	probably benign	0.00
R0964:Col20a1	UTSW	2	180,626,278 (GRCm39)	unclassified	probably benign
R0975:Col20a1	UTSW	2	180,648,619 (GRCm39)	missense	possibly damaging	0.75
R1359:Col20a1	UTSW	2	180,641,585 (GRCm39)	missense	probably benign	0.02
R1395:Col20a1	UTSW	2	180,640,400 (GRCm39)	missense	probably damaging	0.99
R1470:Col20a1	UTSW	2	180,636,753 (GRCm39)	missense	probably benign	0.01
R1470:Col20a1	UTSW	2	180,636,753 (GRCm39)	missense	probably benign	0.01
R1508:Col20a1	UTSW	2	180,634,370 (GRCm39)	missense	probably damaging	0.98
R1865:Col20a1	UTSW	2	180,657,606 (GRCm39)	missense	possibly damaging	0.87
R1883:Col20a1	UTSW	2	180,634,703 (GRCm39)	missense	possibly damaging	0.52
R1884:Col20a1	UTSW	2	180,634,703 (GRCm39)	missense	possibly damaging	0.52
R1906:Col20a1	UTSW	2	180,640,490 (GRCm39)	missense	probably benign	0.00
R2020:Col20a1	UTSW	2	180,654,956 (GRCm39)	critical splice donor site	probably null
R2121:Col20a1	UTSW	2	180,638,249 (GRCm39)	missense	probably damaging	0.99
R2131:Col20a1	UTSW	2	180,634,366 (GRCm39)	missense	probably damaging	1.00
R2343:Col20a1	UTSW	2	180,643,124 (GRCm39)	missense	possibly damaging	0.73
R3153:Col20a1	UTSW	2	180,650,386 (GRCm39)	missense	probably damaging	1.00
R3430:Col20a1	UTSW	2	180,655,078 (GRCm39)	nonsense	probably null
R3547:Col20a1	UTSW	2	180,636,704 (GRCm39)	missense	probably damaging	1.00
R3844:Col20a1	UTSW	2	180,634,242 (GRCm39)	missense	probably damaging	1.00
R3914:Col20a1	UTSW	2	180,640,285 (GRCm39)	missense	probably benign	0.00
R4414:Col20a1	UTSW	2	180,643,043 (GRCm39)	missense	possibly damaging	0.92
R4711:Col20a1	UTSW	2	180,634,284 (GRCm39)	missense	probably damaging	1.00
R4760:Col20a1	UTSW	2	180,626,196 (GRCm39)	unclassified	probably benign
R4771:Col20a1	UTSW	2	180,630,917 (GRCm39)	missense	probably benign	0.17
R4809:Col20a1	UTSW	2	180,640,454 (GRCm39)	missense	probably damaging	1.00
R4872:Col20a1	UTSW	2	180,639,156 (GRCm39)	missense	possibly damaging	0.74
R5045:Col20a1	UTSW	2	180,648,638 (GRCm39)	missense	probably damaging	1.00
R5238:Col20a1	UTSW	2	180,640,379 (GRCm39)	missense	probably damaging	1.00
R6389:Col20a1	UTSW	2	180,634,376 (GRCm39)	splice site	probably null
R6422:Col20a1	UTSW	2	180,656,612 (GRCm39)	missense	possibly damaging	0.75
R6924:Col20a1	UTSW	2	180,638,643 (GRCm39)	missense	probably damaging	1.00
R6982:Col20a1	UTSW	2	180,638,499 (GRCm39)	missense	probably benign	0.00
R7177:Col20a1	UTSW	2	180,636,007 (GRCm39)	nonsense	probably null
R7195:Col20a1	UTSW	2	180,649,024 (GRCm39)	missense	probably damaging	1.00
R7717:Col20a1	UTSW	2	180,649,408 (GRCm39)	missense	probably damaging	1.00
R7872:Col20a1	UTSW	2	180,628,371 (GRCm39)	missense	probably benign	0.14
R8183:Col20a1	UTSW	2	180,640,207 (GRCm39)	missense
R8188:Col20a1	UTSW	2	180,658,126 (GRCm39)	critical splice donor site	probably null
R8331:Col20a1	UTSW	2	180,638,559 (GRCm39)	missense	possibly damaging	0.95
R8423:Col20a1	UTSW	2	180,640,498 (GRCm39)	missense	probably damaging	1.00
R8803:Col20a1	UTSW	2	180,643,131 (GRCm39)	missense	possibly damaging	0.75
R8849:Col20a1	UTSW	2	180,640,432 (GRCm39)	missense	probably damaging	1.00
R8855:Col20a1	UTSW	2	180,655,684 (GRCm39)	missense
R8885:Col20a1	UTSW	2	180,640,296 (GRCm39)	splice site	probably benign
R9160:Col20a1	UTSW	2	180,641,538 (GRCm39)	missense	probably benign
R9223:Col20a1	UTSW	2	180,648,528 (GRCm39)	missense	probably damaging	1.00
R9697:Col20a1	UTSW	2	180,641,577 (GRCm39)	missense	probably benign	0.00

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