Mutagenetix > Incidental Mutation

Incidental Mutation 'R1623:Col25a1'

174766

Institutional Source

Beutler Lab

Gene Symbol

Col25a1

Ensembl Gene

ENSMUSG00000058897

Gene Name

collagen, type XXV, alpha 1

Synonyms

2700062B08Rik

MMRRC Submission

039660-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.136) question?

Stock #

R1623 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

129973992-130393533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 130343699 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 389 (E389G)

Ref Sequence

ENSEMBL: ENSMUSP00000138875 (fasta)

Gene Model

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

AlphaFold

Q99MQ5

Predicted Effect

probably damaging
Transcript: ENSMUST00000080335
AA Change: E389G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: E389G

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: E361G

PolyPhen 2 Score 0.993 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: E361G

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

noncoding transcript
Transcript: ENSMUST00000143830

Predicted Effect

probably damaging
Transcript: ENSMUST00000183368
AA Change: E389G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: E389G

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

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000196743

Coding Region Coverage

1x: 99.0%
3x: 98.0%
10x: 94.9%
20x: 87.6%

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acbd5	A	T	2: 22,984,356 (GRCm39)	D294V	probably damaging	Het
Actn2	A	T	13: 12,355,320 (GRCm39)	I21N	probably benign	Het
Adamts2	C	A	11: 50,558,942 (GRCm39)	P219H	possibly damaging	Het
Atg16l2	A	G	7: 100,939,113 (GRCm39)	F584L	probably benign	Het
Ccdc81	C	T	7: 89,535,390 (GRCm39)	R282Q	probably benign	Het
Ccn4	G	T	15: 66,763,448 (GRCm39)	V12L	possibly damaging	Het
Cd200r3	G	A	16: 44,771,811 (GRCm39)	C25Y	possibly damaging	Het
Cdkl4	C	T	17: 80,863,731 (GRCm39)		probably null	Het
Chrne	T	C	11: 70,509,254 (GRCm39)	E109G	possibly damaging	Het
Clmp	A	G	9: 40,693,856 (GRCm39)	T358A	probably benign	Het
Cmtr1	G	T	17: 29,906,021 (GRCm39)		probably null	Het
Ctc1	C	T	11: 68,911,968 (GRCm39)	T49M	probably damaging	Het
Cyth3	T	A	5: 143,687,127 (GRCm39)	M120K	probably damaging	Het
D430041D05Rik	T	A	2: 103,983,308 (GRCm39)	E1996V	probably damaging	Het
Dnah9	T	C	11: 65,928,463 (GRCm39)	M2069V	probably damaging	Het
Dsg1c	T	C	18: 20,408,234 (GRCm39)	Y428H	probably damaging	Het
Exosc8	T	A	3: 54,641,752 (GRCm39)	T7S	probably damaging	Het
F5	A	G	1: 164,023,191 (GRCm39)	Y1583C	probably damaging	Het
Fam178b	A	G	1: 36,683,405 (GRCm39)	I105T	probably damaging	Het
Fam181a	T	A	12: 103,282,591 (GRCm39)	Y165*	probably null	Het
Fbn2	G	T	18: 58,181,620 (GRCm39)	N1880K	possibly damaging	Het
Gbgt1	A	T	2: 28,394,988 (GRCm39)	M209L	probably benign	Het
Gkn2	C	A	6: 87,355,152 (GRCm39)	Y120*	probably null	Het
Gm14295	T	A	2: 176,499,157 (GRCm39)	D1E	probably damaging	Het
Gpr141	A	T	13: 19,936,082 (GRCm39)		probably null	Het
Gramd2b	C	A	18: 56,565,423 (GRCm39)	P26Q	probably benign	Het
Greb1	A	G	12: 16,724,771 (GRCm39)	I1801T	probably damaging	Het
Gstm3	T	A	3: 107,875,151 (GRCm39)	I64F	possibly damaging	Het
Gtse1	A	G	15: 85,751,779 (GRCm39)	Y324C	probably benign	Het
Hal	C	G	10: 93,352,159 (GRCm39)	T650R	probably benign	Het
Hdac7	G	A	15: 97,706,285 (GRCm39)	Q293*	probably null	Het
Hdlbp	A	T	1: 93,351,591 (GRCm39)	N437K	probably damaging	Het
Hif1an	A	G	19: 44,557,862 (GRCm39)	D248G	probably damaging	Het
Hivep3	T	C	4: 119,952,901 (GRCm39)	S406P	possibly damaging	Het
Hmcn2	A	T	2: 31,348,051 (GRCm39)	D4899V	possibly damaging	Het
Ikzf3	C	T	11: 98,381,157 (GRCm39)		probably null	Het
Inka2	G	A	3: 105,624,136 (GRCm39)	G151D	probably damaging	Het
Itgb4	C	A	11: 115,882,142 (GRCm39)	Y819*	probably null	Het
Itpripl1	T	C	2: 126,983,555 (GRCm39)	D189G	possibly damaging	Het
Kmt2e	A	G	5: 23,687,500 (GRCm39)	Y450C	probably damaging	Het
Mc4r	A	G	18: 66,993,068 (GRCm39)	L15P	probably benign	Het
Mical1	T	G	10: 41,357,389 (GRCm39)		probably null	Het
Mical3	C	T	6: 121,001,768 (GRCm39)	V575M	probably damaging	Het
Mki67	A	T	7: 135,310,547 (GRCm39)		probably null	Het
Mocs2	G	A	13: 114,961,158 (GRCm39)	E52K	probably benign	Het
Myo7b	T	C	18: 32,133,104 (GRCm39)	N415S	probably damaging	Het
Notch1	G	A	2: 26,368,624 (GRCm39)	T555I	possibly damaging	Het
Notch3	T	C	17: 32,358,165 (GRCm39)	D1686G	probably benign	Het
Oit3	A	G	10: 59,264,061 (GRCm39)	F358L	probably damaging	Het
Or10x1	A	C	1: 174,196,515 (GRCm39)	I11L	probably benign	Het
Or6k4	A	T	1: 173,964,883 (GRCm39)	D191V	probably damaging	Het
Orai1	T	A	5: 123,167,265 (GRCm39)	I146N	probably damaging	Het
Pck1	A	G	2: 172,996,511 (GRCm39)	I142V	probably benign	Het
Pdap1	C	T	5: 145,069,739 (GRCm39)	V89M	possibly damaging	Het
Phf11a	T	C	14: 59,525,000 (GRCm39)	D68G	possibly damaging	Het
Pilrb2	T	C	5: 137,869,510 (GRCm39)	N30S	probably damaging	Het
Pkd1	G	A	17: 24,797,243 (GRCm39)	V2551I	probably damaging	Het
Pnpla7	T	C	2: 24,942,611 (GRCm39)	V132A	probably damaging	Het
Prr35	G	A	17: 26,166,508 (GRCm39)	P343L	probably benign	Het
Rad18	C	T	6: 112,605,480 (GRCm39)	S398N	probably damaging	Het
Rdh16f1	C	A	10: 127,626,722 (GRCm39)	N258K	probably benign	Het
Riox2	A	G	16: 59,303,405 (GRCm39)	H240R	probably damaging	Het
Ruvbl1	C	T	6: 88,462,752 (GRCm39)	A292V	probably damaging	Het
Ryr1	C	T	7: 28,794,915 (GRCm39)	G1151S	probably damaging	Het
Serpinb9b	T	C	13: 33,213,548 (GRCm39)	I35T	possibly damaging	Het
Slc1a1	T	A	19: 28,882,122 (GRCm39)	M328K	probably benign	Het
Slc7a13	A	T	4: 19,824,031 (GRCm39)	T267S	possibly damaging	Het
Speer3	G	T	5: 13,846,335 (GRCm39)	M218I	probably benign	Het
Sptan1	A	G	2: 29,876,432 (GRCm39)	I271V	probably damaging	Het
Swap70	A	G	7: 109,863,255 (GRCm39)	T195A	probably benign	Het
Tgs1	T	A	4: 3,585,964 (GRCm39)	N280K	probably benign	Het
Tonsl	A	G	15: 76,522,709 (GRCm39)	C181R	probably damaging	Het
Trdn	A	G	10: 33,134,098 (GRCm39)	K333R	possibly damaging	Het
Trpc4	T	A	3: 54,206,600 (GRCm39)	M600K	probably damaging	Het
Ubr3	C	T	2: 69,808,067 (GRCm39)	Q1183*	probably null	Het
Ubxn4	T	A	1: 128,200,588 (GRCm39)	L360I	possibly damaging	Het
Ugt2b1	T	A	5: 87,074,267 (GRCm39)	T31S	probably benign	Het
Uspl1	T	C	5: 149,152,009 (GRCm39)	S1056P	probably damaging	Het
Vmn2r60	A	T	7: 41,785,279 (GRCm39)	K164*	probably null	Het
Vwce	T	A	19: 10,624,108 (GRCm39)	L333*	probably null	Het
Wdr95	T	A	5: 149,497,581 (GRCm39)	L253Q	probably damaging	Het
Zfp113	T	C	5: 138,143,930 (GRCm39)	M107V	probably benign	Het
Zfp142	T	C	1: 74,610,934 (GRCm39)	T851A	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
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
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'- ACTTGGTGGTCTGTAACACCTTGC -3'
(R):5'- acacacacacacacacacacTCAG -3'

Sequencing Primer
(F):5'- TGCATATAAGCCCTGCTGAG -3'
(R):5'- cacacacacacacTCAGGTTAAG -3'

Posted On

2014-04-24