Mutagenetix > Incidental Mutation

Incidental Mutation 'R7699:Col25a1'

647854

Institutional Source

Beutler Lab

Gene Symbol

Col25a1

Ensembl Gene

ENSMUSG00000058897

Gene Name

collagen, type XXV, alpha 1

Synonyms

2700062B08Rik

MMRRC Submission

045760-MU

Accession Numbers

Essential gene?

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

Stock #

R7699 (G1)

Quality Score

175.009

Status

Validated

Chromosome

Chromosomal Location

129973992-130393533 bp(+) (GRCm39)

Type of Mutation

critical splice donor site (2 bp from exon)

DNA Base Change (assembly)

T to A at 130316128 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000079210 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000080335] [ENSMUST00000080335] [ENSMUST00000080335] [ENSMUST00000106353] [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: 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: 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 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: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.1%

Validation Efficiency

99% (74/75)

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: 74 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts7	C	A	9: 90,070,792 (GRCm39)	P638T	probably damaging	Het
BC005537	C	T	13: 24,987,382 (GRCm39)	R7W	possibly damaging	Het
Bcl2l2	C	T	14: 55,121,836 (GRCm39)		probably benign	Het
Cacna1e	A	T	1: 154,319,674 (GRCm39)	I1404N	probably damaging	Het
Cdc42se1	A	G	3: 95,139,908 (GRCm39)	N35D	probably damaging	Het
Cep290	A	G	10: 100,376,231 (GRCm39)	S1447G	probably benign	Het
Chd6	T	A	2: 160,867,863 (GRCm39)	H436L	probably benign	Het
Cnbd2	T	C	2: 156,217,326 (GRCm39)	V605A	probably benign	Het
Col22a1	T	A	15: 71,845,700 (GRCm39)	D354V	probably damaging	Het
Cttnbp2	T	A	6: 18,514,734 (GRCm39)	M1L	possibly damaging	Het
Cux1	A	T	5: 136,514,593 (GRCm39)		probably null	Het
Cylc2	T	A	4: 51,229,335 (GRCm39)	S226T	unknown	Het
Cyp4b1	T	C	4: 115,499,162 (GRCm39)	D68G	probably benign	Het
Dicer1	A	C	12: 104,671,429 (GRCm39)	L947R	probably damaging	Het
Dmp1	T	C	5: 104,359,590 (GRCm39)	S89P	probably damaging	Het
Dpf1	A	G	7: 29,011,032 (GRCm39)	K144E	possibly damaging	Het
Emc1	T	A	4: 139,082,181 (GRCm39)	H94Q	probably benign	Het
Ep300	C	T	15: 81,470,594 (GRCm39)		probably benign	Het
Epha10	T	C	4: 124,796,440 (GRCm39)	I383T		Het
Epo	T	A	5: 137,483,438 (GRCm39)	E5D	probably benign	Het
Esp15	G	A	17: 39,955,624 (GRCm39)	V64I	possibly damaging	Het
Fbxl18	A	T	5: 142,871,504 (GRCm39)	V577E	probably damaging	Het
Fhl4	A	T	10: 84,934,113 (GRCm39)	C223S	probably damaging	Het
Fhl4	A	T	10: 84,934,379 (GRCm39)	I134N	probably benign	Het
Frmpd2	G	T	14: 33,264,895 (GRCm39)	M891I	probably benign	Het
Gk2	T	C	5: 97,604,257 (GRCm39)	I194V	probably benign	Het
Glt8d2	A	C	10: 82,498,122 (GRCm39)		probably null	Het
Gm12886	G	C	4: 121,273,876 (GRCm39)	H113Q	possibly damaging	Het
Hycc1	A	G	5: 24,120,494 (GRCm39)	S345P	probably damaging	Het
Ighv1-36	A	T	12: 114,843,646 (GRCm39)	Y71*	probably null	Het
Il18bp	A	G	7: 101,666,029 (GRCm39)	W50R	probably damaging	Het
Jmjd1c	T	A	10: 67,054,195 (GRCm39)	I33K	probably benign	Het
Lama5	C	T	2: 179,822,654 (GRCm39)	A2833T	probably damaging	Het
Manea	T	G	4: 26,340,758 (GRCm39)	N68T	probably benign	Het
Map1a	T	C	2: 121,130,201 (GRCm39)	L339P	probably damaging	Het
Mblac1	A	C	5: 138,192,919 (GRCm39)	D87A	probably damaging	Het
Mmp24	C	T	2: 155,640,096 (GRCm39)	T142I	probably damaging	Het
Mpp2	T	A	11: 101,950,261 (GRCm39)	H531L	probably damaging	Het
Mtmr7	G	A	8: 41,059,927 (GRCm39)	A62V	possibly damaging	Het
Mx1	T	A	16: 97,249,521 (GRCm39)	I339F	unknown	Het
Naip2	G	A	13: 100,296,877 (GRCm39)	T1053I	probably benign	Het
Nckap1l	A	G	15: 103,371,248 (GRCm39)		probably null	Het
Or51f23c-ps1	A	G	7: 102,431,529 (GRCm39)	Y282C	possibly damaging	Het
Or5an1b	T	C	19: 12,299,841 (GRCm39)	T117A	probably benign	Het
Otud7b	T	C	3: 96,063,280 (GRCm39)	F840L	probably damaging	Het
Pdzd8	T	C	19: 59,333,373 (GRCm39)	Y216C	probably damaging	Het
Pkd1l1	T	A	11: 8,915,142 (GRCm39)	I133F		Het
Plaur	A	G	7: 24,173,692 (GRCm39)	N221S	possibly damaging	Het
Plin4	T	C	17: 56,410,828 (GRCm39)	T1068A	probably benign	Het
Plxnd1	T	C	6: 115,936,755 (GRCm39)	D1659G	probably damaging	Het
Prpf8	T	A	11: 75,391,022 (GRCm39)	M1357K	probably benign	Het
Prr36	G	T	8: 4,263,989 (GRCm39)	T559N	unknown	Het
Prss46	A	G	9: 110,678,622 (GRCm39)	M2V	probably benign	Het
Rbpms	T	A	8: 34,354,391 (GRCm39)	E51D	probably damaging	Het
Rere	C	T	4: 150,701,555 (GRCm39)	R328W		Het
Retnla	T	A	16: 48,663,176 (GRCm39)	N26K	probably benign	Het
Rubcnl	G	A	14: 75,269,404 (GRCm39)	V21I	probably benign	Het
Safb	T	A	17: 56,908,504 (GRCm39)	S598R	unknown	Het
Sertad4	A	G	1: 192,529,175 (GRCm39)	S214P	possibly damaging	Het
Sin3a	C	T	9: 57,017,938 (GRCm39)	Q786*	probably null	Het
Slc8a3	A	C	12: 81,361,247 (GRCm39)	L524W	probably damaging	Het
Sp3	T	C	2: 72,801,573 (GRCm39)	T191A	probably benign	Het
Sp9	T	C	2: 73,103,724 (GRCm39)	S93P	probably damaging	Het
Tbrg1	A	C	9: 37,560,771 (GRCm39)	H368Q	probably benign	Het
Tinagl1	T	G	4: 130,061,832 (GRCm39)	Q198H	probably benign	Het
Usp19	C	T	9: 108,373,371 (GRCm39)	R648*	probably null	Het
Vmn2r124	A	G	17: 18,293,985 (GRCm39)	M691V	probably benign	Het
Vmn2r2	T	A	3: 64,024,536 (GRCm39)	M682L	possibly damaging	Het
Vps13d	T	A	4: 144,811,975 (GRCm39)	H3344L		Het
Vwa3a	G	A	7: 120,351,841 (GRCm39)	G35E	probably damaging	Het
Zfhx3	A	G	8: 109,677,754 (GRCm39)	S2935G	probably benign	Het
Zfp354c	TCACACTCGGCACA	TCACA	11: 50,706,067 (GRCm39)		probably benign	Het
Zfp758	C	A	17: 22,594,646 (GRCm39)	Y377*	probably null	Het
Zfp952	A	G	17: 33,220,983 (GRCm39)	K67R	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
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'- AATCAGGTCGAAGTCCGTTGG -3'
(R):5'- ACTGCTTGAAAGACTTCTTGTTGG -3'

Sequencing Primer
(F):5'- TGGCTCTGTGAATGATTACAGGAGAC -3'
(R):5'- ACTTTGACAAGCCAGTTTGC -3'

Posted On

2020-09-02