Incidental Mutation 'R7172:Col25a1'
ID 568618
Institutional Source Beutler Lab
Gene Symbol Col25a1
Ensembl Gene ENSMUSG00000058897
Gene Name collagen, type XXV, alpha 1
Synonyms 2700062B08Rik
MMRRC Submission 045264-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.136) question?
Stock # R7172 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 129973992-130393533 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) A to T at 130363981 bp (GRCm39)
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]
AlphaFold Q99MQ5
Predicted Effect silent
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 silent
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: ENSMUST00000183368
AA Change: K537*
SMART Domains Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: K537*

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
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
GeneRefVarChr/LocMutationPredicted EffectZygosity
AA467197 A T 2: 122,480,238 (GRCm39) Y33F probably damaging Het
Abca4 C T 3: 121,897,189 (GRCm39) Q623* probably null Het
Abcb1a A T 5: 8,752,399 (GRCm39) I457F probably benign Het
Abcb9 G A 5: 124,200,869 (GRCm39) Q716* probably null Het
Abhd15 T C 11: 77,406,122 (GRCm39) V33A probably benign Het
Abl2 A G 1: 156,450,157 (GRCm39) D108G probably damaging Het
Adamts3 G A 5: 90,030,860 (GRCm39) probably benign Het
Atmin G T 8: 117,683,281 (GRCm39) V314L probably damaging Het
Axl G T 7: 25,486,399 (GRCm39) Q102K probably benign Het
Cdhr5 A G 7: 140,851,841 (GRCm39) S488P possibly damaging Het
Cnn1 C A 9: 22,016,790 (GRCm39) A126D probably damaging Het
Cxcl2 A G 5: 91,051,879 (GRCm39) T26A probably benign Het
Dcc T C 18: 71,511,755 (GRCm39) T887A probably benign Het
Dhx36 T C 3: 62,408,436 (GRCm39) D134G probably benign Het
Dnah17 T A 11: 117,931,957 (GRCm39) K3672* probably null Het
Fadd G T 7: 144,135,908 (GRCm39) H73Q probably benign Het
Fancm A G 12: 65,152,828 (GRCm39) N1095D possibly damaging Het
Fhod3 T C 18: 25,218,603 (GRCm39) S789P probably damaging Het
Glis2 G A 16: 4,431,339 (GRCm39) V289I probably benign Het
Gm17728 A C 17: 9,641,220 (GRCm39) D110A probably damaging Het
Gm9602 T A 14: 15,933,429 (GRCm39) S45T possibly damaging Het
Gpr137 A G 19: 6,917,049 (GRCm39) S161P possibly damaging Het
Gpr89 C T 3: 96,787,385 (GRCm39) probably null Het
Gps2 C T 11: 69,807,262 (GRCm39) T306I probably benign Het
Hmcn1 A G 1: 150,629,450 (GRCm39) Y936H possibly damaging Het
Hoxa5 A G 6: 52,181,276 (GRCm39) Y19H probably damaging Het
Ifit2 G T 19: 34,550,894 (GRCm39) A145S probably benign Het
Impdh2 G T 9: 108,437,809 (GRCm39) C26F probably benign Het
Kcnh6 T C 11: 105,911,100 (GRCm39) Y552H possibly damaging Het
Kcnma1 A T 14: 23,576,691 (GRCm39) M254K probably damaging Het
Klhdc9 A T 1: 171,188,228 (GRCm39) M1K probably null Het
Klk1b11 A T 7: 43,648,671 (GRCm39) D194V possibly damaging Het
Lama1 A G 17: 68,111,540 (GRCm39) I2264V Het
Lmntd2 A G 7: 140,793,554 (GRCm39) S111P unknown Het
Megf8 T C 7: 25,043,092 (GRCm39) L1338P probably damaging Het
Mipol1 G A 12: 57,372,321 (GRCm39) E127K possibly damaging Het
Mmp25 A T 17: 23,863,762 (GRCm39) C23S probably benign Het
Mup8 A T 4: 60,222,425 (GRCm39) C15* probably null Het
Myh2 A T 11: 67,079,527 (GRCm39) T995S probably benign Het
Myo1d C T 11: 80,483,621 (GRCm39) V863I probably benign Het
N4bp1 A G 8: 87,587,052 (GRCm39) probably null Het
Nat10 G T 2: 103,563,314 (GRCm39) P562T probably damaging Het
Nedd9 C G 13: 41,470,280 (GRCm39) R291P probably benign Het
Nlrc3 G T 16: 3,781,617 (GRCm39) H613Q probably benign Het
Ntn1 A T 11: 68,276,493 (GRCm39) C152S probably damaging Het
Or2av9 T A 11: 58,380,571 (GRCm39) I337F unknown Het
Pam A T 1: 97,762,203 (GRCm39) D793E probably benign Het
Patz1 T G 11: 3,258,032 (GRCm39) V631G probably benign Het
Pcdh15 G A 10: 74,338,597 (GRCm39) V1068M probably damaging Het
Pramel17 A G 4: 101,694,193 (GRCm39) V230A probably benign Het
Prmt5 A G 14: 54,752,343 (GRCm39) F151S possibly damaging Het
Pygo2 G A 3: 89,339,943 (GRCm39) V114I probably benign Het
Rabgap1l A T 1: 160,561,156 (GRCm39) S220R probably benign Het
Rdh7 T G 10: 127,724,218 (GRCm39) S89R possibly damaging Het
Rgsl1 A C 1: 153,701,966 (GRCm39) W163G possibly damaging Het
Ryr3 T A 2: 112,492,002 (GRCm39) N3783I probably damaging Het
Shld2 G A 14: 33,959,525 (GRCm39) T819I probably damaging Het
Slit1 A G 19: 41,623,105 (GRCm39) L644P probably damaging Het
Steap2 A G 5: 5,732,896 (GRCm39) S43P possibly damaging Het
Susd1 A T 4: 59,315,420 (GRCm39) probably null Het
Tbc1d9 A G 8: 83,981,390 (GRCm39) M686V probably damaging Het
Tdrp G A 8: 14,024,579 (GRCm39) R22* probably null Het
Tmem245 A G 4: 56,903,946 (GRCm39) V598A possibly damaging Het
Tnxb A G 17: 34,914,994 (GRCm39) E1994G probably damaging Het
Trcg1 T A 9: 57,155,618 (GRCm39) V757E probably benign Het
Trim10 A G 17: 37,180,955 (GRCm39) E62G possibly damaging Het
Ushbp1 G T 8: 71,841,410 (GRCm39) A473E possibly damaging Het
Vmn1r50 A C 6: 90,084,386 (GRCm39) K44Q possibly damaging Het
Wdr75 A G 1: 45,838,294 (GRCm39) N68D probably damaging Het
Wdr83 A G 8: 85,806,453 (GRCm39) V115A probably damaging Het
Zdhhc17 A G 10: 110,845,809 (GRCm39) L28P possibly damaging Het
Zfp738 C T 13: 67,818,527 (GRCm39) C488Y probably damaging Het
Zfp987 T G 4: 146,058,572 (GRCm39) L50W probably damaging Het
Zfyve28 G T 5: 34,391,753 (GRCm39) R133S probably benign Het
Zscan20 G T 4: 128,479,469 (GRCm39) C1007* probably null 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
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
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'- TACAGAGCAATCCAAGAGCTG -3'
(R):5'- GTGATAGCGCTTAAACTCAGTGTG -3'

Sequencing Primer
(F):5'- GGTAGGTAATAAATAACATCCCACTG -3'
(R):5'- CTCAGTGTGAGTCATGTTGTATTG -3'
Posted On 2019-08-30