Incidental Mutation 'R3818:Col25a1'
ID 274770
Institutional Source Beutler Lab
Gene Symbol Col25a1
Ensembl Gene ENSMUSG00000058897
Gene Name collagen, type XXV, alpha 1
Synonyms 2700062B08Rik
MMRRC Submission 040772-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.136) question?
Stock # R3818 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 129973992-130393533 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 130343720 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Lysine to Arginine at position 396 (K396R)
Ref Sequence ENSEMBL: ENSMUSP00000138875 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000080335] [ENSMUST00000106353] [ENSMUST00000183368]
AlphaFold Q99MQ5
Predicted Effect probably benign
Transcript: ENSMUST00000080335
AA Change: K396R

PolyPhen 2 Score 0.221 (Sensitivity: 0.91; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000079210
Gene: ENSMUSG00000058897
AA Change: K396R

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 benign
Transcript: ENSMUST00000106353
AA Change: K368R

PolyPhen 2 Score 0.074 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000101960
Gene: ENSMUSG00000058897
AA Change: K368R

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: K396R

PolyPhen 2 Score 0.877 (Sensitivity: 0.83; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000138875
Gene: ENSMUSG00000058897
AA Change: K396R

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: ENSMUST00000196743
Meta Mutation Damage Score 0.0659 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.7%
  • 20x: 96.4%
Validation Efficiency 100% (34/34)
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
2310011J03Rik T C 10: 80,155,351 (GRCm39) D54G probably damaging Het
Adra2b G T 2: 127,205,755 (GRCm39) E86* probably null Het
Cachd1 A T 4: 100,848,062 (GRCm39) D1059V probably damaging Het
Cd177 A G 7: 24,453,817 (GRCm39) V358A probably benign Het
Csmd1 C T 8: 16,052,522 (GRCm39) A2201T probably damaging Het
Cyp4a12b A T 4: 115,289,667 (GRCm39) D178V probably damaging Het
Cyp4a30b G T 4: 115,316,206 (GRCm39) A311S probably damaging Het
Dse T C 10: 34,029,429 (GRCm39) I554V probably benign Het
Gabrg3 G A 7: 57,031,412 (GRCm39) Q43* probably null Het
Gjb2 A G 14: 57,337,530 (GRCm39) V226A probably benign Het
Gpr21 C A 2: 37,408,324 (GRCm39) T290N probably damaging Het
Gsdme A C 6: 50,196,391 (GRCm39) S340A probably benign Het
Hivep2 T C 10: 14,019,685 (GRCm39) V2152A possibly damaging Het
Mamdc4 C T 2: 25,455,785 (GRCm39) S840N probably benign Het
Or5p59 A G 7: 107,702,705 (GRCm39) Y63C possibly damaging Het
Or8i2 G A 2: 86,852,054 (GRCm39) T278I probably benign Het
Pah A G 10: 87,357,866 (GRCm39) probably benign Het
Pikfyve T A 1: 65,284,917 (GRCm39) S794T probably damaging Het
Plekhn1 T C 4: 156,309,990 (GRCm39) H108R probably damaging Het
Pomgnt1 T A 4: 116,011,139 (GRCm39) probably null Het
Prkd1 A T 12: 50,466,667 (GRCm39) probably benign Het
Pwp1 C T 10: 85,723,993 (GRCm39) P498L possibly damaging Het
Rasa4 A G 5: 136,131,147 (GRCm39) T414A possibly damaging Het
Rbm26 A T 14: 105,378,706 (GRCm39) L594I probably damaging Het
Rufy4 T C 1: 74,186,822 (GRCm39) C537R probably damaging Het
Skint5 A G 4: 113,486,319 (GRCm39) probably benign Het
Sorcs3 A G 19: 48,592,343 (GRCm39) N336S probably benign Het
Sspo A T 6: 48,458,037 (GRCm39) E3269V possibly damaging Het
Tlr4 A G 4: 66,759,553 (GRCm39) E782G probably benign Het
Tnfrsf11a C T 1: 105,737,085 (GRCm39) T64I probably damaging Het
Top2b T G 14: 16,409,189 (GRCm38) I777M probably damaging Het
Ttl T C 2: 128,934,914 (GRCm39) V358A probably damaging Het
Wdhd1 A G 14: 47,481,258 (GRCm39) probably null Het
Wdr37 A G 13: 8,903,632 (GRCm39) probably benign Het
Zfp939 T C 7: 39,122,792 (GRCm39) noncoding transcript 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
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
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'- AATGAGTCCCTGCTATGATGATATG -3'
(R):5'- CCTCTCTGAATGGAGTTAGGTAAC -3'

Sequencing Primer
(F):5'- TCCCTGCTATGATGATATGTATACTG -3'
(R):5'- AAGAACTGATTCCCACAGGTTCTCTG -3'
Posted On 2015-04-02