Mutagenetix > Incidental Mutation

Incidental Mutation 'R8129:Col25a1'

631889

Institutional Source

Beutler Lab

Gene Symbol

Col25a1

Ensembl Gene

ENSMUSG00000058897

Gene Name

collagen, type XXV, alpha 1

Synonyms

2700062B08Rik

MMRRC Submission

067558-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.100) question?

Stock #

R8129 (G1)

Quality Score

150.008

Status

Validated

Chromosome

Chromosomal Location

129973992-130393533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 130290050 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 247 (S247P)

Ref Sequence

ENSEMBL: ENSMUSP00000079210 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000080335] [ENSMUST00000106353] [ENSMUST00000183368]

AlphaFold

Q99MQ5

Predicted Effect

probably damaging
Transcript: ENSMUST00000080335
AA Change: S247P

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: S247P

Domain	Start	End	E-Value	Type
low complexity region	35	47	N/A	INTRINSIC
Pfam:Collagen	119	165	7e-9	PFAM
low complexity region	188	246	N/A	INTRINSIC
low complexity region	275	288	N/A	INTRINSIC
Pfam:Collagen	311	374	5.4e-11	PFAM
Pfam:Collagen	368	427	2e-9	PFAM
Pfam:Collagen	447	504	1.6e-10	PFAM
Pfam:Collagen	494	561	3.3e-8	PFAM
Pfam:Collagen	586	660	4.3e-11	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000106353
AA Change: S243P

PolyPhen 2 Score 0.988 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: S243P

Domain	Start	End	E-Value	Type
low complexity region	35	47	N/A	INTRINSIC
Pfam:Collagen	119	174	1.7e-11	PFAM
Pfam:Collagen	183	244	6.2e-12	PFAM
Pfam:Collagen	233	297	7.5e-11	PFAM
Pfam:Collagen	294	345	1.8e-9	PFAM
Pfam:Collagen	343	399	1.1e-10	PFAM
Pfam:Collagen	419	475	1.9e-10	PFAM
low complexity region	490	525	N/A	INTRINSIC
Pfam:Collagen	555	622	6e-12	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000183368
AA Change: S247P

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: S247P

Domain	Start	End	E-Value	Type
low complexity region	35	47	N/A	INTRINSIC
Pfam:Collagen	119	165	6.8e-9	PFAM
low complexity region	188	246	N/A	INTRINSIC
internal_repeat_2	249	294	2.8e-5	PROSPERO
internal_repeat_1	294	308	4.06e-8	PROSPERO
Pfam:Collagen	309	372	2.1e-11	PFAM
Pfam:Collagen	371	427	3.7e-10	PFAM
Pfam:Collagen	447	496	7.7e-10	PFAM
low complexity region	497	506	N/A	INTRINSIC
low complexity region	514	527	N/A	INTRINSIC
low complexity region	556	571	N/A	INTRINSIC

Coding Region Coverage

1x: 99.8%
3x: 99.6%
10x: 98.0%
20x: 85.2%

Validation Efficiency

98% (99/101)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a brain-specific membrane associated collagen. A product of proteolytic processing of the encoded protein, CLAC (collagenous Alzheimer amyloid plaque component), binds to amyloid beta-peptides found in Alzheimer amyloid plaques but CLAC inhibits rather than facilitates amyloid fibril elongation (PMID: 16300410). A study of over-expression of this collagen in mice, however, found changes in pathology and behavior suggesting that the encoded protein may promote amyloid plaque formation (PMID: 19548013). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit neonatal lethality, cyanosis and abnormal body curvature with apoptosis of phrenic nerve motor neurons and failure of diaphragm innervation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930402F06Rik	T	C	2: 35,266,187 (GRCm39)	D161G	probably damaging	Het
Adamts19	T	C	18: 59,140,559 (GRCm39)		probably null	Het
Ahnak	A	T	19: 8,977,464 (GRCm39)	M1L	not run	Het
Appl1	A	G	14: 26,671,466 (GRCm39)	S329P	possibly damaging	Het
Bach1	C	T	16: 87,519,314 (GRCm39)	R535W	possibly damaging	Het
Bicc1	T	C	10: 70,915,033 (GRCm39)	D77G	probably benign	Het
Bub1b	T	A	2: 118,468,975 (GRCm39)	D913E	probably benign	Het
Cdhr2	G	T	13: 54,864,208 (GRCm39)		probably null	Het
Commd8	T	C	5: 72,320,164 (GRCm39)	M126V	unknown	Het
Dpysl4	C	T	7: 138,666,076 (GRCm39)	T13M	probably benign	Het
Epc1	A	G	18: 6,439,634 (GRCm39)	V776A	possibly damaging	Het
Fancg	G	T	4: 43,005,036 (GRCm39)		probably null	Het
Fdx1	T	C	9: 51,859,926 (GRCm39)	T135A	probably benign	Het
Fgf7	T	C	2: 125,877,765 (GRCm39)	V44A	probably benign	Het
Fgfr3	A	T	5: 33,891,250 (GRCm39)	M523L	probably damaging	Het
Focad	A	T	4: 88,151,000 (GRCm39)	H548L	unknown	Het
Ftsj3	C	A	11: 106,144,657 (GRCm39)	V111F	probably benign	Het
Gm28168	T	A	1: 117,857,483 (GRCm39)	D12E	probably damaging	Het
Gprin3	T	C	6: 59,330,844 (GRCm39)	T488A	probably benign	Het
Hormad2	C	A	11: 4,296,648 (GRCm39)	V279L	probably benign	Het
Hs6st1	A	G	1: 36,108,105 (GRCm39)	K123E	probably damaging	Het
Ice1	A	G	13: 70,754,320 (GRCm39)	S589P	probably benign	Het
Il1r1	T	A	1: 40,341,447 (GRCm39)	H286Q	probably benign	Het
Il1rl1	T	A	1: 40,490,987 (GRCm39)	C423S	probably damaging	Het
L1td1	A	T	4: 98,621,563 (GRCm39)	M42L	probably benign	Het
Large1	T	C	8: 73,542,585 (GRCm39)	D713G	probably damaging	Het
Llgl2	C	A	11: 115,741,737 (GRCm39)		probably null	Het
Lrp2	C	T	2: 69,260,624 (GRCm39)	V4536M	possibly damaging	Het
Map3k19	A	C	1: 127,750,420 (GRCm39)	L977R	possibly damaging	Het
Myo15a	A	T	11: 60,399,026 (GRCm39)	D1617V		Het
Nek3	A	G	8: 22,639,908 (GRCm39)	I189T	probably damaging	Het
Nrap	C	T	19: 56,355,068 (GRCm39)		probably null	Het
Omd	A	C	13: 49,745,565 (GRCm39)	D325A	probably damaging	Het
Or1x6	G	A	11: 50,939,210 (GRCm39)	R92K	probably benign	Het
Or4a76	C	A	2: 89,460,792 (GRCm39)	G150V	probably damaging	Het
Or52h7	A	G	7: 104,213,584 (GRCm39)	Y52C	probably benign	Het
Or5b118	A	T	19: 13,448,508 (GRCm39)	Y16F	probably damaging	Het
Pabpc6	C	T	17: 9,887,427 (GRCm39)	V375I	possibly damaging	Het
Pcdha5	A	G	18: 37,094,832 (GRCm39)	D447G	probably damaging	Het
Pla2r1	A	T	2: 60,262,944 (GRCm39)	W1032R	probably damaging	Het
Ppp2r5d	T	C	17: 46,995,263 (GRCm39)	Y524C	probably benign	Het
Ppp4r3b	T	C	11: 29,159,364 (GRCm39)	Y573H	probably damaging	Het
Prune2	T	C	19: 17,096,200 (GRCm39)	I568T	probably benign	Het
Ptpn22	G	A	3: 103,797,600 (GRCm39)		probably null	Het
Rbm12b1	A	G	4: 12,145,549 (GRCm39)	D507G	probably damaging	Het
Rdh7	A	G	10: 127,723,370 (GRCm39)	S162P	probably benign	Het
Rreb1	C	T	13: 38,113,775 (GRCm39)	A378V	probably benign	Het
Scaf11	A	G	15: 96,317,350 (GRCm39)	F738S	probably damaging	Het
Sdk1	C	A	5: 142,177,648 (GRCm39)	N2031K	probably benign	Het
Serpina3c	A	T	12: 104,118,056 (GRCm39)	L94Q	probably damaging	Het
Sgo2b	T	C	8: 64,381,834 (GRCm39)	S333G	possibly damaging	Het
Slc22a15	A	G	3: 101,822,658 (GRCm39)	V88A	possibly damaging	Het
Smarcad1	G	T	6: 65,044,078 (GRCm39)	D217Y	probably benign	Het
Sppl2a	A	G	2: 126,765,390 (GRCm39)	F244S	probably damaging	Het
Sspo	G	A	6: 48,443,959 (GRCm39)	D2156N	possibly damaging	Het
Taf2	G	A	15: 54,923,384 (GRCm39)	R298C	probably damaging	Het
Tap2	C	T	17: 34,424,672 (GRCm39)	T135I	probably benign	Het
Tbx15	G	T	3: 99,161,254 (GRCm39)	V20F	probably damaging	Het
Tes	A	T	6: 17,065,242 (GRCm39)		probably benign	Het
Tmem39b	A	T	4: 129,572,468 (GRCm39)	M378K	probably damaging	Het
Trim44	A	G	2: 102,230,848 (GRCm39)	V61A	unknown	Het
Ttll5	T	C	12: 85,937,858 (GRCm39)		probably null	Het
Tubgcp4	C	T	2: 121,004,109 (GRCm39)	T50I	possibly damaging	Het
Txndc17	G	A	11: 72,098,588 (GRCm39)	V47M	probably damaging	Het
Ubp1	A	G	9: 113,804,417 (GRCm39)	E494G	possibly damaging	Het
Utp20	A	T	10: 88,628,487 (GRCm39)	S936T	probably benign	Het
Wdr64	A	G	1: 175,603,154 (GRCm39)	D585G	probably damaging	Het
Wdtc1	A	T	4: 133,031,460 (GRCm39)		probably null	Het
Zfp292	A	G	4: 34,807,386 (GRCm39)	M1891T	probably damaging	Het
Zfp84	A	C	7: 29,475,862 (GRCm39)	I185L	probably benign	Het
Zmym4	A	G	4: 126,808,956 (GRCm39)	F364L	possibly damaging	Het

Other mutations in Col25a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00336:Col25a1	APN	3	129,975,433 (GRCm39)	splice site	probably benign
IGL00570:Col25a1	APN	3	130,340,081 (GRCm39)	splice site	probably benign
IGL01651:Col25a1	APN	3	130,360,134 (GRCm39)	missense	probably benign	0.06
IGL02033:Col25a1	APN	3	130,182,597 (GRCm39)	splice site	probably benign
IGL02117:Col25a1	APN	3	130,313,422 (GRCm39)	splice site	probably benign
IGL02290:Col25a1	APN	3	130,313,460 (GRCm39)	splice site	probably benign
IGL03135:Col25a1	APN	3	130,323,332 (GRCm39)	splice site	probably benign
R0526:Col25a1	UTSW	3	130,270,043 (GRCm39)	missense	probably damaging	1.00
R0602:Col25a1	UTSW	3	130,369,063 (GRCm39)	splice site	probably null
R0670:Col25a1	UTSW	3	130,180,544 (GRCm39)	missense	possibly damaging	0.95
R0830:Col25a1	UTSW	3	130,378,375 (GRCm39)	missense	probably damaging	1.00
R1220:Col25a1	UTSW	3	130,182,574 (GRCm39)	splice site	probably benign
R1623:Col25a1	UTSW	3	130,343,699 (GRCm39)	missense	probably damaging	1.00
R1818:Col25a1	UTSW	3	130,379,386 (GRCm39)	critical splice donor site	probably null
R2142:Col25a1	UTSW	3	130,363,965 (GRCm39)	missense	probably damaging	1.00
R2190:Col25a1	UTSW	3	130,378,364 (GRCm39)	missense	probably damaging	1.00
R2901:Col25a1	UTSW	3	130,340,040 (GRCm39)	missense	probably damaging	1.00
R2902:Col25a1	UTSW	3	130,340,040 (GRCm39)	missense	probably damaging	1.00
R3703:Col25a1	UTSW	3	130,343,682 (GRCm39)	splice site	probably null
R3818:Col25a1	UTSW	3	130,343,720 (GRCm39)	missense	possibly damaging	0.88
R4726:Col25a1	UTSW	3	130,313,430 (GRCm39)	missense	possibly damaging	0.92
R4775:Col25a1	UTSW	3	129,976,468 (GRCm39)	missense	possibly damaging	0.96
R5036:Col25a1	UTSW	3	130,376,978 (GRCm39)	splice site	probably null
R5110:Col25a1	UTSW	3	130,378,374 (GRCm39)	makesense	probably null
R5501:Col25a1	UTSW	3	130,389,312 (GRCm39)	missense	probably benign	0.07
R5686:Col25a1	UTSW	3	130,357,803 (GRCm39)	missense	probably damaging	1.00
R5698:Col25a1	UTSW	3	130,272,632 (GRCm39)	critical splice acceptor site	probably null
R6131:Col25a1	UTSW	3	130,329,114 (GRCm39)	missense	probably damaging	1.00
R6142:Col25a1	UTSW	3	130,376,978 (GRCm39)	splice site	probably benign
R6549:Col25a1	UTSW	3	129,976,444 (GRCm39)	missense	probably benign
R6624:Col25a1	UTSW	3	130,360,100 (GRCm39)	splice site	probably null
R6898:Col25a1	UTSW	3	130,378,377 (GRCm39)	critical splice donor site	probably null
R7030:Col25a1	UTSW	3	130,272,671 (GRCm39)	critical splice donor site	probably null
R7114:Col25a1	UTSW	3	130,389,324 (GRCm39)	missense	probably benign	0.06
R7172:Col25a1	UTSW	3	130,363,981 (GRCm39)	nonsense	probably null
R7179:Col25a1	UTSW	3	130,323,768 (GRCm39)	missense	probably damaging	0.99
R7340:Col25a1	UTSW	3	130,340,006 (GRCm39)	splice site	probably null
R7488:Col25a1	UTSW	3	130,378,350 (GRCm39)	missense	probably damaging	1.00
R7699:Col25a1	UTSW	3	130,316,128 (GRCm39)	critical splice donor site	probably null
R7976:Col25a1	UTSW	3	130,290,075 (GRCm39)	missense	probably damaging	1.00
R8199:Col25a1	UTSW	3	130,345,628 (GRCm39)	missense	probably damaging	1.00
R8524:Col25a1	UTSW	3	130,342,873 (GRCm39)	missense	probably damaging	1.00
R8809:Col25a1	UTSW	3	130,354,466 (GRCm39)	critical splice acceptor site	probably null
R8973:Col25a1	UTSW	3	130,269,275 (GRCm39)	missense	unknown
R9059:Col25a1	UTSW	3	130,268,499 (GRCm39)	missense	unknown
X0028:Col25a1	UTSW	3	130,370,967 (GRCm39)	missense	possibly damaging	0.85
Z1176:Col25a1	UTSW	3	129,976,444 (GRCm39)	frame shift	probably null
Z1177:Col25a1	UTSW	3	130,316,110 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CAGAACACAGTGGATAACGTCTAG -3'
(R):5'- ACAGCGGAAATGTTTTAGTCTGG -3'

Sequencing Primer
(F):5'- GGGAACACAGCCTTAAAAACCTTTG -3'
(R):5'- GGGATTACCGCTTCCCTAAAG -3'

Posted On

2020-06-30