Incidental Mutation 'R4775:Col25a1'
ID 367830
Institutional Source Beutler Lab
Gene Symbol Col25a1
Ensembl Gene ENSMUSG00000058897
Gene Name collagen, type XXV, alpha 1
Synonyms 2700062B08Rik
MMRRC Submission 041991-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.136) question?
Stock # R4775 (G1)
Quality Score 225
Status Not validated
Chromosome 3
Chromosomal Location 129973992-130393533 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 129976468 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Arginine at position 118 (C118R)
Ref Sequence ENSEMBL: ENSMUSP00000138875 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000080335] [ENSMUST00000106353] [ENSMUST00000183368]
AlphaFold Q99MQ5
Predicted Effect unknown
Transcript: ENSMUST00000080335
AA Change: C118R
SMART Domains Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: C118R

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 unknown
Transcript: ENSMUST00000106353
AA Change: C118R
SMART Domains Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: C118R

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 noncoding transcript
Transcript: ENSMUST00000143830
Predicted Effect possibly damaging
Transcript: ENSMUST00000183368
AA Change: C118R

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: C118R

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
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197950
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.6%
  • 20x: 93.4%
Validation Efficiency
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: 65 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acaca A G 11: 84,134,165 (GRCm39) Y426C probably damaging Het
Adam7 A G 14: 68,745,361 (GRCm39) I621T probably benign Het
Adamts1 A T 16: 85,597,278 (GRCm39) Y260* probably null Het
Adgrf1 C T 17: 43,622,054 (GRCm39) L764F probably damaging Het
Afg3l2 G T 18: 67,554,329 (GRCm39) L458M probably damaging Het
Atp9b A G 18: 80,808,984 (GRCm39) probably null Het
C5ar2 A C 7: 15,971,540 (GRCm39) L129R probably damaging Het
Ccdc174 G A 6: 91,867,875 (GRCm39) probably null Het
Cidec T C 6: 113,411,695 (GRCm39) M1V probably null Het
Clec16a G T 16: 10,456,778 (GRCm39) R663L probably damaging Het
Cox6b2 A G 7: 4,755,074 (GRCm39) C67R probably damaging Het
Cspg4b A T 13: 113,454,229 (GRCm39) I92F possibly damaging Het
Cwf19l2 A G 9: 3,430,973 (GRCm39) Y435C probably benign Het
Dapk1 T A 13: 60,897,156 (GRCm39) S792T probably benign Het
Dis3l T A 9: 64,238,190 (GRCm39) N101Y probably benign Het
Dsg4 A G 18: 20,604,184 (GRCm39) T884A possibly damaging Het
Dvl1 T C 4: 155,942,584 (GRCm39) W617R probably benign Het
Eml5 A G 12: 98,768,566 (GRCm39) V1503A probably benign Het
Engase A T 11: 118,373,497 (GRCm39) D280V probably benign Het
F11r T C 1: 171,289,209 (GRCm39) S224P probably damaging Het
Fanca A G 8: 124,023,045 (GRCm39) V564A probably damaging Het
Foxj2 G T 6: 122,810,230 (GRCm39) Q196H probably benign Het
Gle1 T C 2: 29,826,073 (GRCm39) W51R possibly damaging Het
Gm94 A G 18: 43,925,836 (GRCm39) probably null Het
Gm9830 A T 9: 44,375,721 (GRCm39) noncoding transcript Het
Gpaa1 T A 15: 76,218,891 (GRCm39) probably null Het
Grin1 C T 2: 25,182,475 (GRCm39) A929T possibly damaging Het
Grm7 T A 6: 110,891,332 (GRCm39) D188E probably damaging Het
Gtf2ird2 T C 5: 134,242,970 (GRCm39) F395L probably benign Het
Lipo3 C A 19: 33,757,795 (GRCm39) G225C probably damaging Het
Lonrf2 T A 1: 38,857,140 (GRCm39) probably null Het
Marveld2 A G 13: 100,753,303 (GRCm39) probably benign Het
Mpl A G 4: 118,305,777 (GRCm39) L416P probably damaging Het
Mppe1 A G 18: 67,359,930 (GRCm39) L312P possibly damaging Het
Mpzl3 T A 9: 44,977,730 (GRCm39) S113T probably damaging Het
Mylk3 G A 8: 86,085,689 (GRCm39) Q149* probably null Het
Myt1 T A 2: 181,464,470 (GRCm39) I968N probably damaging Het
Ndc80 A G 17: 71,821,265 (GRCm39) Y228H probably damaging Het
Nelfcd T G 2: 174,268,369 (GRCm39) C520G probably damaging Het
Nfrkb C A 9: 31,330,345 (GRCm39) T1199K possibly damaging Het
Nipa2 A G 7: 55,585,611 (GRCm39) I109T probably benign Het
Nlrp4e A G 7: 23,042,525 (GRCm39) T804A probably benign Het
Nsf A T 11: 103,763,419 (GRCm39) I395K possibly damaging Het
Nt5c1b G A 12: 10,425,449 (GRCm39) V331I probably damaging Het
Or13a28 A T 7: 140,217,829 (GRCm39) I72F probably damaging Het
Or1e29 A G 11: 73,667,377 (GRCm39) Y259H probably damaging Het
Pask T C 1: 93,265,246 (GRCm39) D3G probably damaging Het
Pglyrp3 T C 3: 91,933,037 (GRCm39) V110A possibly damaging Het
Ppp4r3a C T 12: 101,019,825 (GRCm39) V377M probably damaging Het
Prr12 A G 7: 44,700,749 (GRCm39) probably benign Het
Ptdss1 G A 13: 67,135,922 (GRCm39) probably null Het
Qser1 A G 2: 104,620,246 (GRCm39) S189P probably damaging Het
Rph3a T A 5: 121,092,551 (GRCm39) Y350F probably benign Het
Skint4 A T 4: 111,993,261 (GRCm39) H328L probably damaging Het
Smyd4 G A 11: 75,282,018 (GRCm39) C497Y probably damaging Het
Stk11ip T C 1: 75,510,497 (GRCm39) W864R possibly damaging Het
Stkld1 T A 2: 26,841,757 (GRCm39) V543E probably damaging Het
Taok2 A G 7: 126,469,940 (GRCm39) S963P probably damaging Het
Tars2 A G 3: 95,653,959 (GRCm39) L354P probably damaging Het
Tns2 C T 15: 102,017,369 (GRCm39) R281C probably damaging Het
Tpcn2 A G 7: 144,821,079 (GRCm39) L325P probably damaging Het
Trappc3l C G 10: 33,974,807 (GRCm39) H96Q probably benign Het
Trim66 A T 7: 109,056,796 (GRCm39) Y1120* probably null Het
Trio G A 15: 27,881,428 (GRCm39) Q548* probably null Het
Wipf2 T A 11: 98,781,558 (GRCm39) D32E 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
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
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'- TCCTTATGCAAGCTATCAGATGC -3'
(R):5'- AGCAGACCTTAGCATGCTG -3'

Sequencing Primer
(F):5'- CAAGCTATCAGATGCTGGCG -3'
(R):5'- CATCTTTTGGACTGAGACATGTTG -3'
Posted On 2015-12-29