Incidental Mutation 'R5408:Xcr1'
ID 426404
Institutional Source Beutler Lab
Gene Symbol Xcr1
Ensembl Gene ENSMUSG00000060509
Gene Name chemokine (C motif) receptor 1
Synonyms GPR5, C motif-1/lymphotactin receptor, Ccxcr1, XCR1
MMRRC Submission 042977-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.078) question?
Stock # R5408 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 123681380-123691094 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 123685631 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Phenylalanine at position 44 (I44F)
Ref Sequence ENSEMBL: ENSMUSP00000138255 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000084715] [ENSMUST00000167595] [ENSMUST00000182350] [ENSMUST00000184082]
AlphaFold Q9R0M1
Predicted Effect probably benign
Transcript: ENSMUST00000084715
SMART Domains Protein: ENSMUSP00000081764
Gene: ENSMUSG00000025241

DomainStartEndE-ValueType
Pfam:RUN 19 167 4.7e-12 PFAM
low complexity region 196 206 N/A INTRINSIC
coiled coil region 223 270 N/A INTRINSIC
coiled coil region 348 1110 N/A INTRINSIC
FYVE 1124 1191 2.69e-16 SMART
PDB:1OLM|E 1343 1428 1e-5 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000167595
SMART Domains Protein: ENSMUSP00000133222
Gene: ENSMUSG00000025241

DomainStartEndE-ValueType
Pfam:RUN 20 167 7.8e-12 PFAM
low complexity region 196 206 N/A INTRINSIC
coiled coil region 223 270 N/A INTRINSIC
coiled coil region 348 1110 N/A INTRINSIC
FYVE 1124 1191 2.69e-16 SMART
PDB:1OLM|E 1343 1428 1e-5 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000182350
AA Change: I44F

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000138255
Gene: ENSMUSG00000060509
AA Change: I44F

DomainStartEndE-ValueType
low complexity region 48 59 N/A INTRINSIC
Pfam:7tm_1 60 295 1.9e-45 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000183700
Predicted Effect probably benign
Transcript: ENSMUST00000184082
SMART Domains Protein: ENSMUSP00000139343
Gene: ENSMUSG00000025241

DomainStartEndE-ValueType
Pfam:RUN 7 167 4.5e-12 PFAM
low complexity region 196 206 N/A INTRINSIC
coiled coil region 223 270 N/A INTRINSIC
low complexity region 355 366 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.4%
  • 20x: 95.6%
Validation Efficiency 99% (74/75)
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 chemokine receptor belonging to the G protein-coupled receptor superfamily. The family members are characterized by the presence of 7 transmembrane domains and numerous conserved amino acids. This receptor is most closely related to RBS11 and the MIP1-alpha/RANTES receptor. It transduces a signal by increasing the intracellular calcium ions level. The viral macrophage inflammatory protein-II is an antagonist of this receptor and blocks signaling. Two alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a targeted null mutation exhibit reduced CD8+ dendritic cell migration in response to XCL1. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
A430110L20Rik A G 1: 181,054,979 (GRCm39) noncoding transcript Het
Actn2 T C 13: 12,285,681 (GRCm39) I837V probably benign Het
Adora1 T A 1: 134,130,901 (GRCm39) T257S probably benign Het
Akap9 T A 5: 4,108,458 (GRCm39) M2954K possibly damaging Het
Akr1c13 G T 13: 4,244,715 (GRCm39) A98S probably benign Het
Aldh2 C T 5: 121,708,620 (GRCm39) probably benign Het
Ank1 A G 8: 23,572,209 (GRCm39) N48D probably damaging Het
Ash1l A G 3: 88,889,701 (GRCm39) T527A probably damaging Het
Atp13a1 T C 8: 70,249,490 (GRCm39) V251A probably benign Het
Baz1a A T 12: 54,969,835 (GRCm39) D608E probably damaging Het
Bend5 A T 4: 111,311,280 (GRCm39) probably null Het
Blm T G 7: 80,152,370 (GRCm39) T526P probably benign Het
Cacna1a T C 8: 85,276,336 (GRCm39) V559A probably damaging Het
Cacna2d4 A G 6: 119,325,752 (GRCm39) D1042G probably damaging Het
Cadps T C 14: 12,705,759 (GRCm38) H212R possibly damaging Het
Cdh3 T C 8: 107,263,269 (GRCm39) I106T probably damaging Het
Cenps C A 4: 149,214,658 (GRCm39) probably benign Het
Cfap68 T C 9: 50,676,057 (GRCm39) N87S probably damaging Het
Col16a1 A T 4: 129,986,898 (GRCm39) probably benign Het
Dctn6 C T 8: 34,562,056 (GRCm39) V89I possibly damaging Het
Dgkz C A 2: 91,766,168 (GRCm39) G798W possibly damaging Het
Epb41l2 A T 10: 25,343,992 (GRCm39) probably null Het
Fam171a2 T C 11: 102,328,344 (GRCm39) K805R possibly damaging Het
Fam89b G T 19: 5,779,421 (GRCm39) Y45* probably null Het
Fchsd2 A G 7: 100,920,781 (GRCm39) N462S possibly damaging Het
Fyco1 T G 9: 123,658,568 (GRCm39) H536P probably damaging Het
Galnt12 A T 4: 47,104,169 (GRCm39) E142D probably damaging Het
Gspt1 C T 16: 11,071,719 (GRCm39) G48D probably benign Het
H6pd A G 4: 150,067,322 (GRCm39) S355P probably damaging Het
Hectd2 T C 19: 36,532,296 (GRCm39) V38A possibly damaging Het
Jup C T 11: 100,267,607 (GRCm39) R572Q probably damaging Het
Kcng3 T C 17: 83,938,434 (GRCm39) D205G probably benign Het
Kif13b A T 14: 65,017,138 (GRCm39) probably null Het
Mapk3 A G 7: 126,363,007 (GRCm39) D253G probably damaging Het
Methig1 A T 15: 100,281,635 (GRCm39) Y253F possibly damaging Het
Mmp3 T C 9: 7,449,904 (GRCm39) S263P probably damaging Het
Mpo T A 11: 87,691,851 (GRCm39) probably null Het
Nbeal2 C A 9: 110,466,588 (GRCm39) G772W possibly damaging Het
Nr1d1 T A 11: 98,661,087 (GRCm39) H393L probably benign Het
Obscn A G 11: 58,942,437 (GRCm39) V4915A probably damaging Het
Olfml2b T A 1: 170,472,545 (GRCm39) W19R probably damaging Het
Or13p4 T C 4: 118,547,641 (GRCm39) T3A probably benign Het
Or56b1b C T 7: 108,164,376 (GRCm39) A209T probably damaging Het
Padi6 G A 4: 140,454,996 (GRCm39) T647I probably damaging Het
Pcyox1 A G 6: 86,369,280 (GRCm39) L113S probably damaging Het
Pde4dip T A 3: 97,704,052 (GRCm39) T192S probably benign Het
Pip4k2a T C 2: 18,911,119 (GRCm39) H87R probably benign Het
Pkd1l3 C A 8: 110,393,684 (GRCm39) T2004N probably damaging Het
Prex1 CGTTGTTGTTGT CGTTGTTGTTGTTGT 2: 166,417,573 (GRCm39) probably benign Het
Ptprz1 C T 6: 23,002,599 (GRCm39) T1563I probably damaging Het
Reg3b T C 6: 78,350,215 (GRCm39) V165A probably benign Het
Rreb1 A G 13: 38,115,320 (GRCm39) D893G probably benign Het
Sap18 A T 14: 58,039,431 (GRCm39) M78L probably benign Het
Scaper A T 9: 55,493,508 (GRCm39) F1226I probably damaging Het
Scyl3 A T 1: 163,782,245 (GRCm39) probably null Het
Shoc2 A G 19: 53,976,556 (GRCm39) M149V probably benign Het
Slc7a2 G A 8: 41,368,042 (GRCm39) R602K probably damaging Het
Sox30 A G 11: 45,882,694 (GRCm39) I575V possibly damaging Het
Trim14 A T 4: 46,507,134 (GRCm39) C361S possibly damaging Het
Ttn T C 2: 76,731,272 (GRCm39) probably benign Het
Uncx A T 5: 139,530,245 (GRCm39) K108* probably null Het
Usp54 A T 14: 20,600,501 (GRCm39) L1412Q probably damaging Het
Uty A G Y: 1,245,614 (GRCm39) V6A possibly damaging Het
Vmn1r30 C T 6: 58,412,029 (GRCm39) V268I probably benign Het
Wdsub1 T C 2: 59,691,887 (GRCm39) probably benign Het
Wipf3 A G 6: 54,458,896 (GRCm39) I84V probably benign Het
Zfp687 T C 3: 94,916,586 (GRCm39) probably benign Het
Zfp729b A T 13: 67,739,563 (GRCm39) S901T probably benign Het
Zhx1 A T 15: 57,915,819 (GRCm39) M809K probably damaging Het
Zswim9 T C 7: 12,994,753 (GRCm39) K468E possibly damaging Het
Other mutations in Xcr1
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL03324:Xcr1 APN 9 123,685,549 (GRCm39) missense probably benign 0.26
R0049:Xcr1 UTSW 9 123,684,940 (GRCm39) missense possibly damaging 0.49
R0049:Xcr1 UTSW 9 123,684,940 (GRCm39) missense possibly damaging 0.49
R0318:Xcr1 UTSW 9 123,685,219 (GRCm39) missense possibly damaging 0.92
R0683:Xcr1 UTSW 9 123,684,940 (GRCm39) missense probably benign 0.03
R4107:Xcr1 UTSW 9 123,685,153 (GRCm39) missense possibly damaging 0.67
R4127:Xcr1 UTSW 9 123,685,561 (GRCm39) missense probably damaging 1.00
R4859:Xcr1 UTSW 9 123,685,712 (GRCm39) missense probably benign
R5419:Xcr1 UTSW 9 123,685,375 (GRCm39) missense probably benign 0.06
R5817:Xcr1 UTSW 9 123,684,922 (GRCm39) missense possibly damaging 0.94
R6051:Xcr1 UTSW 9 123,685,181 (GRCm39) missense probably benign 0.01
R6384:Xcr1 UTSW 9 123,684,847 (GRCm39) missense probably damaging 1.00
R6395:Xcr1 UTSW 9 123,684,854 (GRCm39) missense probably damaging 0.96
R6528:Xcr1 UTSW 9 123,685,048 (GRCm39) missense probably damaging 1.00
R6594:Xcr1 UTSW 9 123,685,309 (GRCm39) missense probably benign 0.00
R6990:Xcr1 UTSW 9 123,685,300 (GRCm39) missense probably benign 0.15
R7648:Xcr1 UTSW 9 123,685,657 (GRCm39) missense possibly damaging 0.54
R9276:Xcr1 UTSW 9 123,685,680 (GRCm39) missense probably benign 0.01
Predicted Primers PCR Primer
(F):5'- GTGCTGAGATCAACACAGGC -3'
(R):5'- TAGTTCACTAGTGGAATCTGGCCC -3'

Sequencing Primer
(F):5'- CTGAGATCAACACAGGCAGTAGAC -3'
(R):5'- GCAGCATGGATAATAATGATCCC -3'
Posted On 2016-09-01