Incidental Mutation 'R5036:Col25a1'
ID 389530
Institutional Source Beutler Lab
Gene Symbol Col25a1
Ensembl Gene ENSMUSG00000058897
Gene Name collagen, type XXV, alpha 1
Synonyms 2700062B08Rik
MMRRC Submission 042627-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.136) question?
Stock # R5036 (G1)
Quality Score 124
Status Validated
Chromosome 3
Chromosomal Location 129973992-130393533 bp(+) (GRCm39)
Type of Mutation splice site (6 bp from exon)
DNA Base Change (assembly) T to C at 130376978 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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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

DomainStartEndE-ValueType
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 0.9755 question?
Coding Region Coverage
  • 1x: 99.0%
  • 3x: 98.2%
  • 10x: 95.7%
  • 20x: 90.1%
Validation Efficiency 100% (44/44)
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: 35 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2610021A01Rik G A 7: 41,275,578 (GRCm39) G427D possibly damaging Het
Agbl5 G A 5: 31,060,403 (GRCm39) R141Q probably damaging Het
C4b T A 17: 34,959,419 (GRCm39) probably null Het
Cabyr A T 18: 12,884,303 (GRCm39) E263D probably damaging Het
Car1 A T 3: 14,841,299 (GRCm39) D45E possibly damaging Het
Dnah6 G T 6: 73,021,674 (GRCm39) S3549R probably benign Het
Dync1h1 A T 12: 110,596,969 (GRCm39) I1639F probably damaging Het
Fhad1 A T 4: 141,648,052 (GRCm39) D271E probably benign Het
Gle1 T C 2: 29,826,223 (GRCm39) S101P probably benign Het
Gm4781 C A 10: 100,232,851 (GRCm39) noncoding transcript Het
Gpatch3 A G 4: 133,305,461 (GRCm39) Y232C probably damaging Het
Gtf2ird2 A G 5: 134,246,349 (GRCm39) N869S probably damaging Het
Ifi204 G A 1: 173,580,311 (GRCm39) P400S possibly damaging Het
Ighv2-2 T C 12: 113,552,092 (GRCm39) T49A possibly damaging Het
Itsn1 T A 16: 91,579,123 (GRCm39) probably benign Het
Mib2 A T 4: 155,740,745 (GRCm39) N626K probably damaging Het
Nf1 C A 11: 79,337,690 (GRCm39) Q1098K probably damaging Het
Odc1 C A 12: 17,598,020 (GRCm39) Q116K probably damaging Het
Otof C T 5: 30,541,783 (GRCm39) E761K possibly damaging Het
Palld A T 8: 62,003,196 (GRCm39) V301D probably damaging Het
Pask A T 1: 93,249,801 (GRCm39) L533* probably null Het
Plekhh2 T C 17: 84,879,189 (GRCm39) S638P probably damaging Het
Scaf8 T A 17: 3,214,537 (GRCm39) probably benign Het
Sdccag8 G T 1: 176,839,541 (GRCm39) R695L probably damaging Het
Serpina1c A G 12: 103,865,085 (GRCm39) I187T probably damaging Het
Slitrk5 G T 14: 111,918,316 (GRCm39) G647W possibly damaging Het
Sycp1 T A 3: 102,727,916 (GRCm39) K899M probably damaging Het
Taok1 G A 11: 77,440,157 (GRCm39) R617C probably benign Het
Tbc1d32 A C 10: 56,071,500 (GRCm39) Y341* probably null Het
Tenm4 A G 7: 96,343,997 (GRCm39) N267D probably damaging Het
Tenm4 T C 7: 96,501,768 (GRCm39) V1287A probably damaging Het
Tsga10 A T 1: 37,823,049 (GRCm39) V488E possibly damaging Het
Ttc39c G T 18: 12,820,138 (GRCm39) probably null Het
Uck1 A T 2: 32,148,478 (GRCm39) probably benign Het
Vmn2r98 A G 17: 19,286,419 (GRCm39) I306V probably benign Het
Other mutations in Col25a1
AlleleSourceChrCoordTypePredicted EffectPPH 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
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'- TTTCAGCAGTCATCTGGCAGC -3'
(R):5'- ATTTGAGGCCGAGTATGATCTG -3'

Sequencing Primer
(F):5'- CTTCGTCACTACAGTCTTGAAGGAG -3'
(R):5'- CCGAGTATGATCTGTCTGTAGCAC -3'
Posted On 2016-06-06