Mutagenetix > Incidental Mutation

Incidental Mutation 'R6422:Col20a1'

518202

Institutional Source

Beutler Lab

Gene Symbol

Col20a1

Ensembl Gene

ENSMUSG00000016356

Gene Name

collagen, type XX, alpha 1

Synonyms

1700051I12Rik

MMRRC Submission

044563-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6422 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

180628328-180660156 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 180656612 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Asparagine at position 1161 (T1161N)

Ref Sequence

ENSEMBL: ENSMUSP00000115291 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000108851] [ENSMUST00000108856] [ENSMUST00000149179] [ENSMUST00000228434]

AlphaFold

Q923P0

Predicted Effect

probably benign
Transcript: ENSMUST00000108851

SMART Domains

Protein: ENSMUSP00000104479
Gene: ENSMUSG00000027577

Domain	Start	End	E-Value	Type
signal peptide	1	30	N/A	INTRINSIC
Pfam:Neur_chan_LBD	39	245	8.4e-79	PFAM
Pfam:Neur_chan_memb	252	620	3.3e-112	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000108856
AA Change: T1235N

PolyPhen 2 Score 0.392 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000104484
Gene: ENSMUSG00000016356
AA Change: T1235N

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

possibly damaging
Transcript: ENSMUST00000149179
AA Change: T1161N

PolyPhen 2 Score 0.754 (Sensitivity: 0.85; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000115291
Gene: ENSMUSG00000016356
AA Change: T1161N

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

unknown
Transcript: ENSMUST00000155425
AA Change: T63N

SMART Domains

Protein: ENSMUSP00000114654
Gene: ENSMUSG00000016356
AA Change: T63N

Domain	Start	End	E-Value	Type
Pfam:Collagen	1	55	4.9e-12	PFAM
Pfam:Collagen	36	94	2.2e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000198922

Predicted Effect

probably benign
Transcript: ENSMUST00000228434
AA Change: T1193N

PolyPhen 2 Score 0.110 (Sensitivity: 0.93; Specificity: 0.86)

Coding Region Coverage

1x: 99.9%
3x: 99.5%
10x: 97.5%
20x: 91.8%

Validation Efficiency

97% (30/31)

Allele List at MGI

Other mutations in this stock

Total: 31 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A430005L14Rik	T	A	4: 154,045,381 (GRCm39)	F137I	probably damaging	Het
Adam11	A	G	11: 102,665,109 (GRCm39)	K417R	possibly damaging	Het
Btbd9	G	A	17: 30,749,230 (GRCm39)	A28V	probably benign	Het
Cabin1	A	G	10: 75,492,626 (GRCm39)	Y1890H	probably damaging	Het
Castor2	T	A	5: 134,164,549 (GRCm39)	M170K	probably benign	Het
Cep162	G	T	9: 87,114,069 (GRCm39)	N334K	possibly damaging	Het
Cep85l	A	T	10: 53,167,876 (GRCm39)	M634K	possibly damaging	Het
Dip2b	T	A	15: 100,096,892 (GRCm39)	D1155E	probably damaging	Het
Dlst	T	A	12: 85,177,659 (GRCm39)		probably null	Het
Dsc1	A	C	18: 20,228,090 (GRCm39)	L422R	probably damaging	Het
Gcn1	T	C	5: 115,747,603 (GRCm39)	W1699R	probably damaging	Het
Gm14443	G	A	2: 175,012,174 (GRCm39)	Q91*	probably null	Het
Gm8159	T	C	14: 15,850,210 (GRCm39)	I143T	probably damaging	Het
Il4i1	G	T	7: 44,489,560 (GRCm39)	A442S	probably damaging	Het
Kif26a	T	G	12: 112,135,309 (GRCm39)	L337R	possibly damaging	Het
Lat2	T	C	5: 134,632,015 (GRCm39)	D144G	probably benign	Het
Ndst1	G	T	18: 60,836,025 (GRCm39)	H419Q	probably benign	Het
Notch4	T	C	17: 34,803,533 (GRCm39)	I1484T	probably benign	Het
Or51v14	T	G	7: 103,261,221 (GRCm39)	E113A	probably damaging	Het
Paxbp1	A	T	16: 90,820,332 (GRCm39)	M697K	probably benign	Het
Plxnb1	A	G	9: 108,937,992 (GRCm39)	Y1246C	probably damaging	Het
Prr5	C	T	15: 84,578,005 (GRCm39)	R96C	probably damaging	Het
Ptpn7	G	T	1: 135,062,240 (GRCm39)	C62F	probably damaging	Het
Rsrc1	C	T	3: 66,901,982 (GRCm39)	P44L	unknown	Het
Sall2	A	C	14: 52,550,181 (GRCm39)	*1003G	probably null	Het
Slc5a4b	C	A	10: 75,939,696 (GRCm39)	V147F	probably damaging	Het
Snapc4	A	G	2: 26,258,315 (GRCm39)	W702R	probably benign	Het
Tbc1d32	A	T	10: 55,904,157 (GRCm39)	C1203*	probably null	Het
Tmprss11d	T	A	5: 86,457,284 (GRCm39)	Y125F	probably damaging	Het
Tpp1	G	A	7: 105,396,163 (GRCm39)	T512I	probably benign	Het
Tyw5	G	A	1: 57,440,570 (GRCm39)	A64V	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
R5566:Col20a1	UTSW	2	180,628,316 (GRCm39)	splice site	probably null
R6389:Col20a1	UTSW	2	180,634,376 (GRCm39)	splice site	probably null
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'- GGTTTGGGGACAGAACTCAG -3'
(R):5'- AAGCTGCTGAGACCCTATTTC -3'

Sequencing Primer
(F):5'- TTTGGGGACAGAACTCAGAACATG -3'
(R):5'- AGCTGGCTCCTCATAAGTCAG -3'

Posted On

2018-05-24