Mutagenetix > Incidental Mutation

Incidental Mutation 'R7179:Col25a1'

558825

Institutional Source

Beutler Lab

Gene Symbol

Col25a1

Ensembl Gene

ENSMUSG00000058897

Gene Name

collagen, type XXV, alpha 1

Synonyms

2700062B08Rik

MMRRC Submission

045269-MU

Accession Numbers

Essential gene?

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

Stock #

R7179 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

129973992-130393533 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to T at 130323768 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Leucine at position 321 (R321L)

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: R321L

PolyPhen 2 Score 0.990 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: R321L

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: R308L

PolyPhen 2 Score 0.961 (Sensitivity: 0.78; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: R308L

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: R321L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: R321L

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

Meta Mutation Damage Score

0.2317

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.1%

Validation Efficiency

100% (76/76)

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acot13	A	T	13: 25,002,154 (GRCm39)	I96K	probably benign	Het
Adam6a	A	G	12: 113,509,291 (GRCm39)	T555A	probably benign	Het
Alms1	C	T	6: 85,598,351 (GRCm39)	P1059L	probably benign	Het
Apol7c	T	C	15: 77,409,843 (GRCm39)	T368A	probably benign	Het
Arfgef3	A	T	10: 18,475,015 (GRCm39)	L1557Q	probably damaging	Het
Baz2a	C	T	10: 127,960,326 (GRCm39)	R1514W	probably damaging	Het
Bmp3	T	A	5: 99,020,622 (GRCm39)	D348E	probably damaging	Het
Bves	A	G	10: 45,230,913 (GRCm39)	S295G	probably damaging	Het
Carmil1	A	G	13: 24,204,052 (GRCm39)	C1328R	probably benign	Het
Ccnk	T	A	12: 108,153,517 (GRCm39)	Y93N	probably damaging	Het
Ccr1	A	T	9: 123,764,089 (GRCm39)	V147D	probably damaging	Het
Cd24a	G	A	10: 43,458,636 (GRCm39)	G36S	probably benign	Het
Cep104	A	G	4: 154,077,324 (GRCm39)	Y569C	probably damaging	Het
Chd2	A	T	7: 73,125,168 (GRCm39)	I884N	probably damaging	Het
Cnst	A	T	1: 179,406,947 (GRCm39)		probably benign	Het
Col22a1	A	G	15: 71,805,262 (GRCm39)	L146P	unknown	Het
Ctnnd2	T	C	15: 30,683,510 (GRCm39)	Y504H	possibly damaging	Het
D3Ertd751e	C	A	3: 41,703,143 (GRCm39)	Q73K	probably damaging	Het
Dsc2	C	T	18: 20,168,332 (GRCm39)		probably null	Het
Eya1	A	T	1: 14,373,076 (GRCm39)	S14R	probably damaging	Het
Fam131c	A	T	4: 141,110,328 (GRCm39)		probably null	Het
Flvcr2	T	C	12: 85,793,965 (GRCm39)	F114L	possibly damaging	Het
Fyn	A	G	10: 39,408,120 (GRCm39)	D321G	possibly damaging	Het
Galnt5	A	C	2: 57,888,621 (GRCm39)	M74L	probably benign	Het
Garin4	G	A	1: 190,896,218 (GRCm39)	R142C	probably damaging	Het
Gas2l2	G	A	11: 83,313,288 (GRCm39)	P675S	probably benign	Het
Gm9508	G	T	10: 77,532,470 (GRCm39)	Q200K	unknown	Het
Greb1l	G	A	18: 10,544,576 (GRCm39)	S1390N	probably benign	Het
Hdac5	G	T	11: 102,095,385 (GRCm39)	T430K	possibly damaging	Het
Hjurp	TCTGGGAGGGCTTGCTCCGGGGGCAGTGTGTCCTGTTCTTGTGCAGCCCCTGCT	TCT	1: 88,194,000 (GRCm39)		probably benign	Het
Khnyn	C	T	14: 56,131,811 (GRCm39)	P578S	probably damaging	Het
Lepr	A	T	4: 101,602,856 (GRCm39)	T215S	probably benign	Het
Lrfn5	G	A	12: 61,890,768 (GRCm39)	V686I	probably benign	Het
Mapkap1	T	A	2: 34,408,712 (GRCm39)	H233Q	possibly damaging	Het
Mcm3	A	G	1: 20,885,081 (GRCm39)	I201T	probably damaging	Het
Metrnl	G	A	11: 121,606,734 (GRCm39)	R263Q	probably damaging	Het
Mettl22	A	G	16: 8,295,924 (GRCm39)	E71G	probably benign	Het
Muc16	T	C	9: 18,553,304 (GRCm39)	T4330A	probably benign	Het
Mug1	A	G	6: 121,834,379 (GRCm39)	T387A	probably benign	Het
Myh4	A	G	11: 67,135,550 (GRCm39)	D379G	probably benign	Het
Nbas	A	G	12: 13,455,398 (GRCm39)	D1204G	possibly damaging	Het
Ncor2	T	C	5: 125,132,847 (GRCm39)	K478E	unknown	Het
Or14a256	A	T	7: 86,265,574 (GRCm39)	L93Q	possibly damaging	Het
Or51d1	A	G	7: 102,347,477 (GRCm39)	T11A	probably benign	Het
Or5k1	T	A	16: 58,617,250 (GRCm39)	I320F	probably benign	Het
Osbpl7	G	A	11: 96,941,662 (GRCm39)	V62I	probably benign	Het
Pak1ip1	A	G	13: 41,163,018 (GRCm39)	N246S	probably damaging	Het
Prim1	A	G	10: 127,851,845 (GRCm39)	Y39C	probably damaging	Het
Prl3b1	G	T	13: 27,427,827 (GRCm39)	V46L	probably benign	Het
Prss54	A	T	8: 96,292,199 (GRCm39)	S127T	probably benign	Het
Rasal3	G	A	17: 32,611,391 (GRCm39)	T912M	probably damaging	Het
Rrp12	T	A	19: 41,872,217 (GRCm39)	T420S	probably benign	Het
Rspo1	A	G	4: 124,898,831 (GRCm39)	N51D	probably damaging	Het
Rufy4	A	G	1: 74,172,035 (GRCm39)	R253G	probably benign	Het
Scaf1	G	A	7: 44,657,167 (GRCm39)	R571C	unknown	Het
Scn2a	A	T	2: 65,532,323 (GRCm39)	H645L	probably damaging	Het
Sec24b	A	G	3: 129,782,595 (GRCm39)	S1132P	probably damaging	Het
Slc1a2	A	G	2: 102,586,290 (GRCm39)	K298R	probably damaging	Het
Slc25a54	T	A	3: 109,014,573 (GRCm39)	N230K	probably benign	Het
Slc27a4	T	G	2: 29,705,664 (GRCm39)	Y617*	probably null	Het
Slc2a10	T	C	2: 165,357,269 (GRCm39)	S310P	probably damaging	Het
Snx33	C	T	9: 56,833,151 (GRCm39)	R306H	probably damaging	Het
Spag9	A	T	11: 93,980,258 (GRCm39)		probably null	Het
Spg11	A	T	2: 121,932,270 (GRCm39)		probably null	Het
Sycp2l	A	G	13: 41,283,258 (GRCm39)	T165A	probably damaging	Het
Syt14	A	G	1: 192,615,571 (GRCm39)	C189R	probably damaging	Het
Taar9	A	T	10: 23,984,882 (GRCm39)	L184Q	probably damaging	Het
Tkt	C	T	14: 30,281,815 (GRCm39)	P111L	probably damaging	Het
Trpc1	A	T	9: 95,603,197 (GRCm39)	L445Q	possibly damaging	Het
Usp53	A	G	3: 122,743,359 (GRCm39)	S526P	probably benign	Het
Vps54	T	G	11: 21,248,791 (GRCm39)	W447G	probably damaging	Het
Xirp2	A	T	2: 67,340,177 (GRCm39)	H806L	probably benign	Het
Zfp451	A	T	1: 33,841,651 (GRCm39)	H410Q	unknown	Het
Zfp688	A	G	7: 127,018,484 (GRCm39)	C214R	probably damaging	Het
Zic4	A	G	9: 91,261,174 (GRCm39)	D143G	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
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'- GGTTTCCAAGTGCCAAGCAAG -3'
(R):5'- TTCATACTTGGCTATGCTTGGC -3'

Sequencing Primer
(F):5'- CACGGCAATTTCCATATGCGTAG -3'
(R):5'- AACTGCACCATTGTGCA -3'

Posted On

2019-06-26