Mutagenetix > Incidental Mutation

Incidental Mutation 'R1818:Col25a1'

204572

Institutional Source

Beutler Lab

Gene Symbol

Col25a1

Ensembl Gene

ENSMUSG00000058897

Gene Name

collagen, type XXV, alpha 1

Synonyms

2700062B08Rik

MMRRC Submission

039846-MU

Accession Numbers

Essential gene?

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

Stock #

R1818 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

129973992-130393533 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (1 bp from exon)

DNA Base Change (assembly)

G to A at 130379386 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000101960 (fasta)

Gene Model

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

AlphaFold

Q99MQ5

Predicted Effect

probably null
Transcript: ENSMUST00000080335

SMART Domains

Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897

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 null
Transcript: ENSMUST00000106353

SMART Domains

Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897

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 null
Transcript: ENSMUST00000106353

SMART Domains

Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897

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 benign
Transcript: ENSMUST00000183368

SMART Domains

Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897

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: 97.3%
3x: 96.6%
10x: 94.5%
20x: 90.4%

Validation Efficiency

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: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aass	T	A	6: 23,075,857 (GRCm39)		probably null	Het
Adam6b	T	A	12: 113,454,876 (GRCm39)	N564K	probably benign	Het
Ahi1	A	G	10: 20,864,461 (GRCm39)	Y731C	probably damaging	Het
Ankk1	A	G	9: 49,331,725 (GRCm39)	Y190H	probably benign	Het
Ankmy1	T	A	1: 92,814,553 (GRCm39)	D318V	probably benign	Het
Ankrd33b	G	A	15: 31,367,267 (GRCm39)	A91V	probably damaging	Het
Ap3b1	A	G	13: 94,608,212 (GRCm39)	N561S	possibly damaging	Het
Apob	A	G	12: 8,056,834 (GRCm39)	N1739S	probably damaging	Het
Apob	A	G	12: 8,063,064 (GRCm39)	T236A	possibly damaging	Het
Birc6	G	A	17: 74,956,844 (GRCm39)	A3593T	probably damaging	Het
Bnc2	A	G	4: 84,210,111 (GRCm39)	F778L	possibly damaging	Het
Capn2	T	A	1: 182,300,162 (GRCm39)	K609N	probably benign	Het
Car9	G	T	4: 43,512,439 (GRCm39)		probably null	Het
Card11	A	T	5: 140,871,315 (GRCm39)	D729E	probably benign	Het
Ccl20	A	G	1: 83,095,529 (GRCm39)	Y30C	probably damaging	Het
Cd209a	G	A	8: 3,795,576 (GRCm39)	T106I	probably damaging	Het
Cebpz	A	G	17: 79,242,805 (GRCm39)	L283P	probably damaging	Het
Cecr2	A	G	6: 120,708,228 (GRCm39)	T77A	probably damaging	Het
Clec4e	T	A	6: 123,262,452 (GRCm39)	D155V	possibly damaging	Het
Cyp2j11	A	T	4: 96,185,976 (GRCm39)	V403D	probably damaging	Het
Cyp4v3	G	A	8: 45,768,673 (GRCm39)	R296C	possibly damaging	Het
Ddx59	A	G	1: 136,360,245 (GRCm39)	I420V	probably damaging	Het
Denr	T	A	5: 124,055,283 (GRCm39)	D49E	probably benign	Het
Dnaaf3	A	T	7: 4,526,568 (GRCm39)		probably null	Het
Dnaaf3	G	T	7: 4,526,569 (GRCm39)	L503M	probably benign	Het
Dnah7a	A	C	1: 53,598,307 (GRCm39)	D1409E	probably benign	Het
Dnai4	A	G	4: 102,929,854 (GRCm39)	V56A	possibly damaging	Het
Efcab3	T	A	11: 104,612,333 (GRCm39)	L652Q	probably benign	Het
Ehd4	C	T	2: 119,932,885 (GRCm39)	W180*	probably null	Het
Ephb2	A	G	4: 136,382,647 (GRCm39)	S984P	probably benign	Het
Eva1a	T	C	6: 82,048,125 (GRCm39)	M1T	probably null	Het
Fam90a1a	C	G	8: 22,453,787 (GRCm39)	P381A	possibly damaging	Het
Fam90a1a	C	A	8: 22,453,788 (GRCm39)	P381Q	probably damaging	Het
Flnc	T	C	6: 29,457,447 (GRCm39)	Y2382H	probably damaging	Het
Flrt1	A	T	19: 7,072,711 (GRCm39)	L612Q	probably damaging	Het
Fubp1	T	A	3: 151,927,806 (GRCm39)	N419K	probably damaging	Het
Gin1	A	G	1: 97,712,951 (GRCm39)		probably null	Het
Gm4847	T	A	1: 166,465,788 (GRCm39)	H267L	probably damaging	Het
Golga4	T	G	9: 118,402,055 (GRCm39)	V91G	probably damaging	Het
Hip1r	T	C	5: 124,134,018 (GRCm39)		probably null	Het
Ice2	A	G	9: 69,339,383 (GRCm39)	S967G	probably benign	Het
Il18rap	A	G	1: 40,570,687 (GRCm39)	I210V	probably benign	Het
Impdh2	T	G	9: 108,440,411 (GRCm39)		probably null	Het
Inmt	C	A	6: 55,150,404 (GRCm39)	V78F	possibly damaging	Het
Inpp5e	T	C	2: 26,287,886 (GRCm39)	S637G	probably benign	Het
Kansl1	T	C	11: 104,233,283 (GRCm39)	H748R	possibly damaging	Het
Kif28	T	C	1: 179,533,319 (GRCm39)	K541E	possibly damaging	Het
Kifc1	G	A	17: 34,103,685 (GRCm39)	R195C	probably benign	Het
Kifc2	T	C	15: 76,550,281 (GRCm39)	V480A	probably damaging	Het
Lrrc74a	T	C	12: 86,784,484 (GRCm39)	Y71H	probably damaging	Het
Ly75	T	G	2: 60,142,121 (GRCm39)	T1330P	probably damaging	Het
Macf1	A	G	4: 123,270,210 (GRCm39)	V6647A	probably damaging	Het
Mgat1	T	C	11: 49,152,111 (GRCm39)	I198T	possibly damaging	Het
Morc3	A	G	16: 93,652,398 (GRCm39)	Y367C	probably damaging	Het
Mtfr1	A	G	3: 19,269,837 (GRCm39)	T162A	probably damaging	Het
Myrip	C	T	9: 120,217,228 (GRCm39)	S49L	probably damaging	Het
Nup153	A	T	13: 46,835,113 (GRCm39)	N1397K	possibly damaging	Het
Or5h26	T	C	16: 58,988,243 (GRCm39)	K88E	probably benign	Het
Or6x1	T	C	9: 40,098,558 (GRCm39)	V49A	probably benign	Het
Or8b36	T	C	9: 37,937,803 (GRCm39)	S234P	probably damaging	Het
Or8g21	T	C	9: 38,905,902 (GRCm39)	I276M	possibly damaging	Het
Pabpc2	G	T	18: 39,907,163 (GRCm39)	V143L	probably damaging	Het
Pals2	T	G	6: 50,140,411 (GRCm39)	F144V	probably benign	Het
Panx3	T	C	9: 37,575,322 (GRCm39)	K180R	probably benign	Het
Patj	G	A	4: 98,511,885 (GRCm39)	V144M	possibly damaging	Het
Pde1c	T	A	6: 56,103,877 (GRCm39)	K651*	probably null	Het
Pde4c	A	G	8: 71,179,638 (GRCm39)	H63R	probably benign	Het
Pdha2	T	A	3: 140,916,960 (GRCm39)	K183*	probably null	Het
Pkd1l3	T	A	8: 110,375,038 (GRCm39)	C1504S	probably benign	Het
Plbd2	A	T	5: 120,625,574 (GRCm39)		probably null	Het
Poteg	G	A	8: 27,940,195 (GRCm39)	W121*	probably null	Het
Prf1	C	A	10: 61,138,762 (GRCm39)	T240N	probably damaging	Het
Ptprf	A	G	4: 118,067,068 (GRCm39)	Y1883H	probably damaging	Het
Puf60	T	C	15: 75,943,323 (GRCm39)	T322A	possibly damaging	Het
Rev3l	A	G	10: 39,704,420 (GRCm39)	I281M	probably benign	Het
Rufy1	T	C	11: 50,305,399 (GRCm39)	I305V	probably benign	Het
Shisa9	A	C	16: 12,085,426 (GRCm39)	Q329P	probably damaging	Het
Siglech	G	A	7: 55,418,332 (GRCm39)	R100Q	probably damaging	Het
Slc13a5	T	A	11: 72,144,169 (GRCm39)	Y303F	probably benign	Het
Snx6	C	T	12: 54,830,259 (GRCm39)	V67I	possibly damaging	Het
Spef2	C	T	15: 9,584,194 (GRCm39)	E1624K	probably damaging	Het
Tecpr2	A	G	12: 110,892,888 (GRCm39)	Y310C	probably damaging	Het
Top1	T	A	2: 160,557,643 (GRCm39)	L575Q	probably damaging	Het
Usp16	C	T	16: 87,276,020 (GRCm39)	R452*	probably null	Het
Utrn	A	G	10: 12,585,708 (GRCm39)		probably null	Het
Vps13b	G	A	15: 35,877,723 (GRCm39)	G2899E	probably benign	Het
Wipi2	T	A	5: 142,643,963 (GRCm39)	L115Q	probably damaging	Het
Zbtb7c	A	C	18: 76,270,596 (GRCm39)	E228A	probably damaging	Het
Zfp26	T	C	9: 20,353,487 (GRCm39)	T101A	probably benign	Het
Zfp593	A	T	4: 133,972,394 (GRCm39)		probably null	Het
Zfp646	G	A	7: 127,482,292 (GRCm39)	G1490S	probably benign	Het
Zfp948	G	A	17: 21,805,069 (GRCm39)	V20M	probably damaging	Het
Zranb3	A	T	1: 127,945,293 (GRCm39)		probably null	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
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
R8129:Col25a1	UTSW	3	130,290,050 (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'- AAGCGCTACTGTTCTTTGTAAG -3'
(R):5'- TTGGAACACAGGATGGACAC -3'

Sequencing Primer
(F):5'- AGTTTAAAGGTTATTTGGCATGTCAG -3'
(R):5'- CACGGGAAAGGTGCCTG -3'

Posted On

2014-06-23