Mutagenetix > Incidental Mutations

Incidental Mutation 'R7172:Col25a1'

568618

Institutional Source

Beutler Lab

Gene Symbol

Col25a1

Ensembl Gene

ENSMUSG00000058897

Gene Name

collagen, type XXV, alpha 1

Synonyms

2700062B08Rik

MMRRC Submission

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.104) question?

Stock #

R7172 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

130131501-130599877 bp(+) (GRCm38)

Type of Mutation

nonsense

DNA Base Change (assembly)

A to T at 130570332 bp

Zygosity

Heterozygous

Amino Acid Change

Lysine to Stop codon at position 537 (K537*)

Ref Sequence

ENSEMBL: ENSMUSP00000138875 (fasta)

Gene Model

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

Predicted Effect

silent
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

silent
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: ENSMUST00000183368
AA Change: K537*

SMART Domains

Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: K537*

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: 99.6%
20x: 98.7%

Validation Efficiency

100% (74/74)

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
AA467197	A	T	2: 122,638,318	Y33F	probably damaging	Het
Abca4	C	T	3: 122,103,540	Q623*	probably null	Het
Abcb1a	A	T	5: 8,702,399	I457F	probably benign	Het
Abcb9	G	A	5: 124,062,806	Q716*	probably null	Het
Abhd15	T	C	11: 77,515,296	V33A	probably benign	Het
Abl2	A	G	1: 156,622,587	D108G	probably damaging	Het
Adamts3	G	A	5: 89,883,001		probably benign	Het
Atmin	G	T	8: 116,956,542	V314L	probably damaging	Het
Axl	G	T	7: 25,786,974	Q102K	probably benign	Het
B020004J07Rik	A	G	4: 101,836,996	V230A	probably benign	Het
Cdhr5	A	G	7: 141,271,928	S488P	possibly damaging	Het
Cnn1	C	A	9: 22,105,494	A126D	probably damaging	Het
Cxcl2	A	G	5: 90,904,020	T26A	probably benign	Het
Dcc	T	C	18: 71,378,684	T887A	probably benign	Het
Dhx36	T	C	3: 62,501,015	D134G	probably benign	Het
Dnah17	T	A	11: 118,041,131	K3672*	probably null	Het
Fadd	G	T	7: 144,582,171	H73Q	probably benign	Het
Fam35a	G	A	14: 34,237,568	T819I	probably damaging	Het
Fancm	A	G	12: 65,106,054	N1095D	possibly damaging	Het
Fhod3	T	C	18: 25,085,546	S789P	probably damaging	Het
Glis2	G	A	16: 4,613,475	V289I	probably benign	Het
Gm17728	A	C	17: 9,422,388	D110A	probably damaging	Het
Gm9602	T	A	14: 4,777,282	S45T	possibly damaging	Het
Gpr137	A	G	19: 6,939,681	S161P	possibly damaging	Het
Gpr89	C	T	3: 96,880,069		probably null	Het
Gps2	C	T	11: 69,916,436	T306I	probably benign	Het
Hmcn1	A	G	1: 150,753,699	Y936H	possibly damaging	Het
Hoxa5	A	G	6: 52,204,296	Y19H	probably damaging	Het
Ifit2	G	T	19: 34,573,494	A145S	probably benign	Het
Impdh2	G	T	9: 108,560,610	C26F	probably benign	Het
Kcnh6	T	C	11: 106,020,274	Y552H	possibly damaging	Het
Kcnma1	A	T	14: 23,526,623	M254K	probably damaging	Het
Klhdc9	A	T	1: 171,360,660	M1K	probably null	Het
Klk1b11	A	T	7: 43,999,247	D194V	possibly damaging	Het
Lama1	A	G	17: 67,804,545	I2264V		Het
Lmntd2	A	G	7: 141,213,641	S111P	unknown	Het
Megf8	T	C	7: 25,343,667	L1338P	probably damaging	Het
Mipol1	G	A	12: 57,325,535	E127K	possibly damaging	Het
Mmp25	A	T	17: 23,644,788	C23S	probably benign	Het
Mup8	A	T	4: 60,222,425	C15*	probably null	Het
Myh2	A	T	11: 67,188,701	T995S	probably benign	Het
Myo1d	C	T	11: 80,592,795	V863I	probably benign	Het
N4bp1	A	G	8: 86,860,424		probably null	Het
Nat10	G	T	2: 103,732,969	P562T	probably damaging	Het
Nedd9	C	G	13: 41,316,804	R291P	probably benign	Het
Nlrc3	G	T	16: 3,963,753	H613Q	probably benign	Het
Ntn1	A	T	11: 68,385,667	C152S	probably damaging	Het
Olfr332	T	A	11: 58,489,745	I337F	unknown	Het
Pam	A	T	1: 97,834,478	D793E	probably benign	Het
Patz1	T	G	11: 3,308,032	V631G	probably benign	Het
Pcdh15	G	A	10: 74,502,765	V1068M	probably damaging	Het
Prmt5	A	G	14: 54,514,886	F151S	possibly damaging	Het
Pygo2	G	A	3: 89,432,636	V114I	probably benign	Het
Rabgap1l	A	T	1: 160,733,586	S220R	probably benign	Het
Rdh7	T	G	10: 127,888,349	S89R	possibly damaging	Het
Rgsl1	A	C	1: 153,826,220	W163G	possibly damaging	Het
Ryr3	T	A	2: 112,661,657	N3783I	probably damaging	Het
Slit1	A	G	19: 41,634,666	L644P	probably damaging	Het
Steap2	A	G	5: 5,682,896	S43P	possibly damaging	Het
Susd1	A	T	4: 59,315,420		probably null	Het
Tbc1d9	A	G	8: 83,254,761	M686V	probably damaging	Het
Tdrp	G	A	8: 13,974,579	R22*	probably null	Het
Tmem245	A	G	4: 56,903,946	V598A	possibly damaging	Het
Tnxb	A	G	17: 34,696,020	E1994G	probably damaging	Het
Trcg1	T	A	9: 57,248,335	V757E	probably benign	Het
Trim10	A	G	17: 36,870,063	E62G	possibly damaging	Het
Ushbp1	G	T	8: 71,388,766	A473E	possibly damaging	Het
Vmn1r50	A	C	6: 90,107,404	K44Q	possibly damaging	Het
Wdr75	A	G	1: 45,799,134	N68D	probably damaging	Het
Wdr83	A	G	8: 85,079,824	V115A	probably damaging	Het
Zdhhc17	A	G	10: 111,009,948	L28P	possibly damaging	Het
Zfp738	C	T	13: 67,670,408	C488Y	probably damaging	Het
Zfp987	T	G	4: 146,122,002	L50W	probably damaging	Het
Zfyve28	G	T	5: 34,234,409	R133S	probably benign	Het
Zscan20	G	T	4: 128,585,676	C1007*	probably null	Het

Other mutations in Col25a1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00336:Col25a1	APN	3	130181784	splice site	probably benign
IGL00570:Col25a1	APN	3	130546432	splice site	probably benign
IGL01651:Col25a1	APN	3	130566485	missense	probably benign	0.06
IGL02033:Col25a1	APN	3	130388948	splice site	probably benign
IGL02117:Col25a1	APN	3	130519773	splice site	probably benign
IGL02290:Col25a1	APN	3	130519811	splice site	probably benign
IGL03135:Col25a1	APN	3	130529683	splice site	probably benign
R0526:Col25a1	UTSW	3	130476394	missense	probably damaging	1.00
R0602:Col25a1	UTSW	3	130575414	splice site	probably null
R0670:Col25a1	UTSW	3	130386895	missense	possibly damaging	0.95
R0830:Col25a1	UTSW	3	130584726	missense	probably damaging	1.00
R1220:Col25a1	UTSW	3	130388925	splice site	probably benign
R1623:Col25a1	UTSW	3	130550050	missense	probably damaging	1.00
R1818:Col25a1	UTSW	3	130585737	critical splice donor site	probably null
R2142:Col25a1	UTSW	3	130570316	missense	probably damaging	1.00
R2190:Col25a1	UTSW	3	130584715	missense	probably damaging	1.00
R2901:Col25a1	UTSW	3	130546391	missense	probably damaging	1.00
R2902:Col25a1	UTSW	3	130546391	missense	probably damaging	1.00
R3703:Col25a1	UTSW	3	130550033	splice site	probably null
R3818:Col25a1	UTSW	3	130550071	missense	possibly damaging	0.88
R4726:Col25a1	UTSW	3	130519781	missense	possibly damaging	0.92
R4775:Col25a1	UTSW	3	130182819	missense	possibly damaging	0.96
R5036:Col25a1	UTSW	3	130583329	splice site	probably null
R5110:Col25a1	UTSW	3	130584725	makesense	probably null
R5501:Col25a1	UTSW	3	130595663	missense	probably benign	0.07
R5686:Col25a1	UTSW	3	130564154	missense	probably damaging	1.00
R5698:Col25a1	UTSW	3	130478983	critical splice acceptor site	probably null
R6131:Col25a1	UTSW	3	130535465	missense	probably damaging	1.00
R6142:Col25a1	UTSW	3	130583329	splice site	probably benign
R6549:Col25a1	UTSW	3	130182795	missense	probably benign
R6624:Col25a1	UTSW	3	130566451	splice site	probably null
R6898:Col25a1	UTSW	3	130584728	critical splice donor site	probably null
R7030:Col25a1	UTSW	3	130479022	critical splice donor site	probably null
R7114:Col25a1	UTSW	3	130595675	missense	probably benign	0.06
R7179:Col25a1	UTSW	3	130530119	missense	probably damaging	0.99
R7340:Col25a1	UTSW	3	130546357	splice site	probably null
R7488:Col25a1	UTSW	3	130584701	missense	probably damaging	1.00
R7699:Col25a1	UTSW	3	130522479	critical splice donor site	probably null
R7976:Col25a1	UTSW	3	130496426	missense	probably damaging	1.00
R8129:Col25a1	UTSW	3	130496401	missense	probably damaging	1.00
R8199:Col25a1	UTSW	3	130551979	missense	probably damaging	1.00
R8524:Col25a1	UTSW	3	130549224	missense	probably damaging	1.00
X0028:Col25a1	UTSW	3	130577318	missense	possibly damaging	0.85
Z1176:Col25a1	UTSW	3	130182795	frame shift	probably null
Z1177:Col25a1	UTSW	3	130522461	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TACAGAGCAATCCAAGAGCTG -3'
(R):5'- GTGATAGCGCTTAAACTCAGTGTG -3'

Sequencing Primer
(F):5'- GGTAGGTAATAAATAACATCCCACTG -3'
(R):5'- CTCAGTGTGAGTCATGTTGTATTG -3'

Posted On

2019-08-30