Incidental Mutation 'R3980:Ccr9'
ID 311264
Institutional Source Beutler Lab
Gene Symbol Ccr9
Ensembl Gene ENSMUSG00000029530
Gene Name C-C motif chemokine receptor 9
Synonyms GPR-9-6, Cmkbr10
MMRRC Submission 040843-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.135) question?
Stock # R3980 (G1)
Quality Score 225
Status Not validated
Chromosome 9
Chromosomal Location 123596276-123612522 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to T at 123608441 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Asparagine to Isoleucine at position 41 (N41I)
Ref Sequence ENSEMBL: ENSMUSP00000137144 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000111454] [ENSMUST00000163559] [ENSMUST00000166236] [ENSMUST00000168910] [ENSMUST00000180093]
AlphaFold Q9WUT7
Predicted Effect probably benign
Transcript: ENSMUST00000111454
AA Change: N29I

PolyPhen 2 Score 0.067 (Sensitivity: 0.94; Specificity: 0.84)
SMART Domains Protein: ENSMUSP00000107081
Gene: ENSMUSG00000029530
AA Change: N29I

DomainStartEndE-ValueType
Pfam:7TM_GPCR_Srsx 47 320 1.2e-5 PFAM
Pfam:7tm_1 53 305 1.1e-51 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000163559
AA Change: N41I

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000131782
Gene: ENSMUSG00000029530
AA Change: N41I

DomainStartEndE-ValueType
Pfam:7TM_GPCR_Srsx 59 332 5.9e-6 PFAM
Pfam:7tm_1 65 317 3.4e-52 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000166236
AA Change: N41I

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000127024
Gene: ENSMUSG00000029530
AA Change: N41I

DomainStartEndE-ValueType
Pfam:7TM_GPCR_Srsx 59 332 5.9e-6 PFAM
Pfam:7tm_1 65 317 4.6e-47 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000168910
AA Change: N41I

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000126758
Gene: ENSMUSG00000029530
AA Change: N41I

DomainStartEndE-ValueType
Pfam:7TM_GPCR_Srsx 59 332 5.9e-6 PFAM
Pfam:7tm_1 65 317 3.4e-52 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000172093
Predicted Effect probably benign
Transcript: ENSMUST00000180093
AA Change: N41I

PolyPhen 2 Score 0.143 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000137144
Gene: ENSMUSG00000029530
AA Change: N41I

DomainStartEndE-ValueType
Pfam:7TM_GPCR_Srsx 59 332 5.9e-6 PFAM
Pfam:7tm_1 65 317 3.4e-52 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000214413
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.5%
  • 10x: 97.2%
  • 20x: 94.8%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the beta chemokine receptor family. It is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. Chemokines and their receptors are key regulators of the thymocytes migration and maturation in normal and inflammation conditions. The specific ligand of this receptor is CCL25. It has been found that this gene is differentially expressed by T lymphocytes of small intestine and colon, suggested a role in the thymocytes recruitment and development that may permit functional specialization of immune responses in different segment of the gastrointestinal tract. This gene is mapped to the chemokine receptor gene cluster region. Two alternatively spliced transcript variants have been described. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
PHENOTYPE: Homozygous null mice have altered trafficing of lymphocytes to the intestine. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrb1 G A 15: 74,454,792 (GRCm39) G268R probably damaging Het
Amacr T A 15: 10,989,015 (GRCm39) Y240* probably null Het
Ankhd1 A T 18: 36,780,666 (GRCm39) H1906L probably damaging Het
Arhgef25 C A 10: 127,023,089 (GRCm39) C106F probably damaging Het
Bean1 A T 8: 104,937,730 (GRCm39) Q103L possibly damaging Het
Ceacam16 A G 7: 19,592,558 (GRCm39) F117L probably benign Het
Col4a1 T C 8: 11,289,155 (GRCm39) probably benign Het
Csk A G 9: 57,538,063 (GRCm39) Y48H probably damaging Het
Csmd1 T A 8: 15,956,056 (GRCm39) K3384* probably null Het
Ctnnd2 T A 15: 30,669,589 (GRCm39) H399Q probably benign Het
Cutal T C 2: 34,772,325 (GRCm39) Y30H possibly damaging Het
Cybb T C X: 9,310,827 (GRCm39) Y425C probably damaging Het
Dab2 A G 15: 6,464,644 (GRCm39) probably null Het
Defb30 C A 14: 63,273,421 (GRCm39) C64F probably damaging Het
Eif2a T C 3: 58,446,960 (GRCm39) I45T probably benign Het
Esyt1 T A 10: 128,347,393 (GRCm39) D1044V probably damaging Het
Gabpb2 A T 3: 95,096,081 (GRCm39) V382E probably damaging Het
Glb1 T A 9: 114,246,132 (GRCm39) I61K probably damaging Het
Insyn2b G A 11: 34,352,678 (GRCm39) C240Y probably benign Het
Kcnt1 T C 2: 25,783,226 (GRCm39) V263A possibly damaging Het
Kdm5b A G 1: 134,547,408 (GRCm39) D1019G probably benign Het
Klhl2 A T 8: 65,196,109 (GRCm39) L545M probably damaging Het
Klhl2 C A 8: 65,196,115 (GRCm39) G543C probably damaging Het
Krt31 G T 11: 99,939,030 (GRCm39) Q264K probably damaging Het
Lmnb1 A G 18: 56,864,091 (GRCm39) D232G probably damaging Het
Loxhd1 T C 18: 77,501,855 (GRCm39) F859L probably damaging Het
Map7 C A 10: 20,143,099 (GRCm39) T416K unknown Het
Med18 T A 4: 132,190,251 (GRCm39) I45F probably benign Het
Mn1 A T 5: 111,569,636 (GRCm39) H1202L possibly damaging Het
Mpp7 T C 18: 7,444,062 (GRCm39) D120G probably benign Het
Nlrp1b A T 11: 71,072,437 (GRCm39) F469I possibly damaging Het
Nos3 T A 5: 24,582,929 (GRCm39) D685E probably damaging Het
Nrap G A 19: 56,369,984 (GRCm39) A206V probably benign Het
Nuggc T C 14: 65,856,542 (GRCm39) probably null Het
Oasl1 C T 5: 115,070,957 (GRCm39) T274I probably damaging Het
Or10ak12 T A 4: 118,666,500 (GRCm39) Y187F probably benign Het
Or51a25 T C 7: 102,372,959 (GRCm39) N246S probably damaging Het
Parp3 T C 9: 106,351,267 (GRCm39) D278G probably damaging Het
Phc3 T A 3: 30,991,080 (GRCm39) Q346L probably damaging Het
Pigo A G 4: 43,019,231 (GRCm39) L1029P probably damaging Het
Plcb3 A G 19: 6,943,803 (GRCm39) I66T probably damaging Het
Plch2 T C 4: 155,069,255 (GRCm39) S1019G probably benign Het
Plekhg6 C A 6: 125,350,146 (GRCm39) C264F probably damaging Het
Plxna2 C T 1: 194,431,625 (GRCm39) S538F probably damaging Het
Pou4f2 G T 8: 79,162,067 (GRCm39) H179N possibly damaging Het
Prpf39 T C 12: 65,108,231 (GRCm39) probably benign Het
Rapgef1 G A 2: 29,609,662 (GRCm39) V700I probably benign Het
Rdh14 A G 12: 10,444,703 (GRCm39) I185V probably benign Het
Rnf111 A T 9: 70,349,607 (GRCm39) H785Q probably damaging Het
Rttn C T 18: 89,035,399 (GRCm39) R758W probably benign Het
Sik3 G A 9: 46,113,361 (GRCm39) V601M probably damaging Het
Slc22a14 T C 9: 119,007,552 (GRCm39) T286A probably benign Het
Slc36a3 G A 11: 55,026,209 (GRCm39) T203I probably benign Het
Spata31 A T 13: 65,070,468 (GRCm39) Q872L probably benign Het
Spata31d1c A G 13: 65,182,974 (GRCm39) D172G possibly damaging Het
Sphkap A T 1: 83,245,215 (GRCm39) probably null Het
Stat6 T C 10: 127,491,248 (GRCm39) V463A probably damaging Het
Stx7 T C 10: 24,060,947 (GRCm39) S225P probably damaging Het
Sult2a7 A T 7: 14,207,334 (GRCm39) probably benign Het
Tada2a A T 11: 83,993,946 (GRCm39) F179L probably benign Het
Tas2r103 A G 6: 133,013,280 (GRCm39) L262P probably benign Het
Tfap2d A G 1: 19,236,187 (GRCm39) I382V possibly damaging Het
Tshr C A 12: 91,504,517 (GRCm39) A485D probably damaging Het
Vmn1r32 T A 6: 66,530,698 (GRCm39) Y26F probably damaging Het
Vmn1r5 A G 6: 56,962,636 (GRCm39) T104A probably damaging Het
Wbp1l T A 19: 46,642,396 (GRCm39) probably null Het
Other mutations in Ccr9
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00402:Ccr9 APN 9 123,609,109 (GRCm39) missense probably benign 0.00
IGL00983:Ccr9 APN 9 123,608,351 (GRCm39) missense probably benign
IGL02466:Ccr9 APN 9 123,608,911 (GRCm39) missense probably damaging 1.00
IGL03151:Ccr9 APN 9 123,603,638 (GRCm39) utr 5 prime probably benign
IGL03302:Ccr9 APN 9 123,608,601 (GRCm39) missense probably damaging 1.00
hamlet UTSW 9 123,608,504 (GRCm39) missense probably damaging 1.00
Laertes UTSW 9 123,608,911 (GRCm39) missense probably damaging 1.00
Ophelia UTSW 9 123,608,534 (GRCm39) missense probably damaging 1.00
R0310:Ccr9 UTSW 9 123,603,617 (GRCm39) utr 5 prime probably benign
R0393:Ccr9 UTSW 9 123,609,035 (GRCm39) missense probably benign 0.18
R0421:Ccr9 UTSW 9 123,608,671 (GRCm39) missense probably benign
R2069:Ccr9 UTSW 9 123,608,429 (GRCm39) missense probably benign 0.05
R4645:Ccr9 UTSW 9 123,608,658 (GRCm39) missense probably benign 0.00
R4672:Ccr9 UTSW 9 123,608,752 (GRCm39) missense probably damaging 0.96
R4920:Ccr9 UTSW 9 123,608,504 (GRCm39) missense probably damaging 1.00
R5661:Ccr9 UTSW 9 123,609,164 (GRCm39) missense probably benign 0.04
R5964:Ccr9 UTSW 9 123,608,499 (GRCm39) missense probably benign 0.12
R7037:Ccr9 UTSW 9 123,609,036 (GRCm39) missense possibly damaging 0.52
R7500:Ccr9 UTSW 9 123,608,534 (GRCm39) missense probably damaging 1.00
R7620:Ccr9 UTSW 9 123,608,911 (GRCm39) missense probably damaging 1.00
R7670:Ccr9 UTSW 9 123,608,371 (GRCm39) missense probably damaging 0.98
R7762:Ccr9 UTSW 9 123,609,022 (GRCm39) missense probably benign 0.08
R8154:Ccr9 UTSW 9 123,608,896 (GRCm39) missense probably benign 0.00
R8283:Ccr9 UTSW 9 123,608,696 (GRCm39) missense probably damaging 1.00
R8525:Ccr9 UTSW 9 123,608,732 (GRCm39) missense probably benign 0.31
R9046:Ccr9 UTSW 9 123,608,831 (GRCm39) missense probably benign
R9273:Ccr9 UTSW 9 123,609,085 (GRCm39) missense probably benign 0.07
R9462:Ccr9 UTSW 9 123,608,600 (GRCm39) missense probably damaging 1.00
X0026:Ccr9 UTSW 9 123,608,566 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- TAGCACTTTGGGTCAGTTTATCC -3'
(R):5'- TTGACCAGCAGCAGCAATGG -3'

Sequencing Primer
(F):5'- GGTCAGTTTATCCTATTTACCATCAG -3'
(R):5'- CAGCAGCAATGGCCCAG -3'
Posted On 2015-04-29