Incidental Mutation 'R2090:Crtam'
ID 231719
Institutional Source Beutler Lab
Gene Symbol Crtam
Ensembl Gene ENSMUSG00000032021
Gene Name cytotoxic and regulatory T cell molecule
Synonyms class I-restricted T cell-associated molecule
MMRRC Submission 040095-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.059) question?
Stock # R2090 (G1)
Quality Score 225
Status Validated
Chromosome 9
Chromosomal Location 40880987-40915922 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 40895612 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Arginine at position 41 (Q41R)
Ref Sequence ENSEMBL: ENSMUSP00000137749 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000034519] [ENSMUST00000180384] [ENSMUST00000180872] [ENSMUST00000188848]
AlphaFold Q149L7
Predicted Effect probably benign
Transcript: ENSMUST00000034519
AA Change: Q231R

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000034519
Gene: ENSMUSG00000032021
AA Change: Q231R

DomainStartEndE-ValueType
IG 21 113 4.7e-9 SMART
Pfam:C2-set_2 119 205 2.7e-16 PFAM
low complexity region 222 239 N/A INTRINSIC
transmembrane domain 283 305 N/A INTRINSIC
low complexity region 326 345 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000180384
AA Change: Q238R

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000137837
Gene: ENSMUSG00000032021
AA Change: Q238R

DomainStartEndE-ValueType
IG 21 113 4.7e-9 SMART
Pfam:C2-set_2 119 205 4.2e-15 PFAM
low complexity region 229 246 N/A INTRINSIC
transmembrane domain 290 312 N/A INTRINSIC
low complexity region 333 352 N/A INTRINSIC
Predicted Effect possibly damaging
Transcript: ENSMUST00000180872
AA Change: Q41R

PolyPhen 2 Score 0.766 (Sensitivity: 0.85; Specificity: 0.92)
SMART Domains Protein: ENSMUSP00000137749
Gene: ENSMUSG00000032021
AA Change: Q41R

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
low complexity region 32 49 N/A INTRINSIC
transmembrane domain 92 114 N/A INTRINSIC
low complexity region 136 155 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000188848
AA Change: Q238R

PolyPhen 2 Score 0.049 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000139826
Gene: ENSMUSG00000032021
AA Change: Q238R

DomainStartEndE-ValueType
IG 21 113 4.7e-9 SMART
Pfam:C2-set_2 119 205 1.9e-15 PFAM
low complexity region 229 246 N/A INTRINSIC
transmembrane domain 289 311 N/A INTRINSIC
low complexity region 332 351 N/A INTRINSIC
Meta Mutation Damage Score 0.1185 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.4%
  • 20x: 95.5%
Validation Efficiency 100% (67/67)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The CRTAM gene is upregulated in CD4 (see MIM 186940)-positive and CD8 (see CD8A; MIM 186910)-positive T cells and encodes a type I transmembrane protein with V and C1-like Ig domains (Yeh et al., 2008 [PubMed 18329370]).[supplied by OMIM, Feb 2009]
PHENOTYPE: Homozygous null mice have defects in late stage T cell activation that leads to less production of inflammatory cytokines, higher proliferation, and an increase in T cell number with age. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adam32 A G 8: 25,391,456 (GRCm39) probably null Het
Adcy7 A T 8: 89,042,485 (GRCm39) T451S probably damaging Het
Adgrg3 A T 8: 95,766,558 (GRCm39) T410S possibly damaging Het
Alg11 G T 8: 22,555,646 (GRCm39) L302F possibly damaging Het
Ankrd17 A G 5: 90,445,905 (GRCm39) V310A possibly damaging Het
Atg16l2 C T 7: 100,942,575 (GRCm39) probably null Het
B3gnt2 A G 11: 22,786,291 (GRCm39) V299A probably benign Het
Birc6 A G 17: 74,969,791 (GRCm39) N4258S probably benign Het
C2cd4d A G 3: 94,271,321 (GRCm39) K196E probably benign Het
Calhm6 A G 10: 34,002,358 (GRCm39) S242P probably damaging Het
Cdr2l A G 11: 115,281,827 (GRCm39) K111E probably damaging Het
Cspp1 A G 1: 10,160,493 (GRCm39) K560R possibly damaging Het
Dcaf15 A T 8: 84,824,400 (GRCm39) Y571* probably null Het
Defa39 A T 8: 22,192,805 (GRCm39) W64R possibly damaging Het
Dpy19l4 T C 4: 11,304,344 (GRCm39) Y99C probably benign Het
Edem3 C T 1: 151,680,577 (GRCm39) probably benign Het
Enpp6 A T 8: 47,518,405 (GRCm39) probably null Het
Foxf2 T A 13: 31,810,824 (GRCm39) D254E probably benign Het
Gjb5 T C 4: 127,249,794 (GRCm39) N117D probably benign Het
Glmn G A 5: 107,709,794 (GRCm39) L337F probably damaging Het
Gsdmc2 T A 15: 63,698,675 (GRCm39) Y307F probably benign Het
Gsdmc3 T A 15: 63,738,631 (GRCm39) M144L probably benign Het
Ibtk A G 9: 85,603,046 (GRCm39) I653T probably benign Het
Il24 T G 1: 130,812,574 (GRCm39) D99A possibly damaging Het
Intu A G 3: 40,637,966 (GRCm39) Q484R probably benign Het
Iqca1l A G 5: 24,755,674 (GRCm39) S283P probably benign Het
Lsp1 T C 7: 142,045,544 (GRCm39) probably benign Het
Mad1l1 A G 5: 139,995,011 (GRCm39) S672P probably benign Het
Man2a2 A T 7: 80,013,858 (GRCm39) probably benign Het
Morc3 C A 16: 93,663,341 (GRCm39) H515N probably benign Het
Nav1 T C 1: 135,534,903 (GRCm39) probably benign Het
Ndor1 A G 2: 25,139,230 (GRCm39) L247P probably damaging Het
Nfkbiz A T 16: 55,636,818 (GRCm39) F494L probably benign Het
Nr1d1 G A 11: 98,661,436 (GRCm39) P277S probably damaging Het
Nrg2 T C 18: 36,151,496 (GRCm39) D682G probably benign Het
Nrros C T 16: 31,962,975 (GRCm39) W311* probably null Het
Oasl1 G A 5: 115,073,993 (GRCm39) D301N probably damaging Het
Or10ag56 A T 2: 87,139,762 (GRCm39) I230F probably benign Het
Or14a258 A T 7: 86,035,289 (GRCm39) I193N probably benign Het
Or5h26 A G 16: 58,988,503 (GRCm39) M1T probably null Het
Palmd A G 3: 116,721,083 (GRCm39) S123P probably damaging Het
Patj A G 4: 98,325,560 (GRCm39) probably benign Het
Pcsk4 T C 10: 80,161,655 (GRCm39) D162G probably benign Het
Plppr5 A G 3: 117,369,520 (GRCm39) D59G possibly damaging Het
Pmvk A C 3: 89,369,189 (GRCm39) R11S possibly damaging Het
Pnliprp1 A G 19: 58,728,901 (GRCm39) T363A probably benign Het
Poll A T 19: 45,547,277 (GRCm39) I65N probably benign Het
Prox1 T A 1: 189,893,009 (GRCm39) S479C probably damaging Het
Prss50 A T 9: 110,691,361 (GRCm39) S222C probably damaging Het
Rasa3 A C 8: 13,632,381 (GRCm39) probably benign Het
Sec14l3 T C 11: 4,025,481 (GRCm39) V335A probably benign Het
Setbp1 C T 18: 78,899,935 (GRCm39) S1244N probably benign Het
Sgcg A T 14: 61,483,213 (GRCm39) F63I probably damaging Het
Skp2 C A 15: 9,113,786 (GRCm39) G376C probably damaging Het
Slc2a13 T A 15: 91,400,695 (GRCm39) I176F probably benign Het
Smc6 A G 12: 11,339,987 (GRCm39) T432A probably benign Het
Snx25 G A 8: 46,509,150 (GRCm39) P478L probably damaging Het
Taf2 A T 15: 54,879,882 (GRCm39) H1151Q probably damaging Het
Thsd1 A G 8: 22,749,673 (GRCm39) K795R possibly damaging Het
Tmem108 G A 9: 103,361,976 (GRCm39) L537F possibly damaging Het
Ubr3 T C 2: 69,766,361 (GRCm39) Y410H probably damaging Het
Vav3 T C 3: 109,555,055 (GRCm39) probably null Het
Vmn1r224 T C 17: 20,639,524 (GRCm39) Y34H probably benign Het
Zeb1 T C 18: 5,766,458 (GRCm39) V323A possibly damaging Het
Zfp652 A G 11: 95,644,834 (GRCm39) D240G probably benign Het
Zfp963 A T 8: 70,195,996 (GRCm39) C152* probably null Het
Other mutations in Crtam
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02883:Crtam APN 9 40,905,797 (GRCm39) missense probably benign
R0722:Crtam UTSW 9 40,903,912 (GRCm39) missense probably damaging 1.00
R1423:Crtam UTSW 9 40,884,918 (GRCm39) missense probably benign 0.36
R1859:Crtam UTSW 9 40,884,900 (GRCm39) missense possibly damaging 0.71
R1935:Crtam UTSW 9 40,915,846 (GRCm39) missense probably benign 0.34
R1936:Crtam UTSW 9 40,915,846 (GRCm39) missense probably benign 0.34
R2360:Crtam UTSW 9 40,884,811 (GRCm39) makesense probably null
R4812:Crtam UTSW 9 40,895,621 (GRCm39) missense probably damaging 0.99
R5995:Crtam UTSW 9 40,905,836 (GRCm39) missense possibly damaging 0.75
R6021:Crtam UTSW 9 40,901,477 (GRCm39) missense probably damaging 1.00
R7428:Crtam UTSW 9 40,892,478 (GRCm39) missense probably benign 0.24
R8750:Crtam UTSW 9 40,895,641 (GRCm39) missense probably benign 0.16
R9632:Crtam UTSW 9 40,895,671 (GRCm39) missense probably benign 0.12
R9710:Crtam UTSW 9 40,895,671 (GRCm39) missense probably benign 0.12
RF044:Crtam UTSW 9 40,895,650 (GRCm39) frame shift probably null
RF057:Crtam UTSW 9 40,895,650 (GRCm39) frame shift probably null
Predicted Primers PCR Primer
(F):5'- ATCAACCTTTGGTTCCACACAAG -3'
(R):5'- TTACACATAGAGGCCCCAGC -3'

Sequencing Primer
(F):5'- GGTTCCACACAAGTATACAAGTG -3'
(R):5'- TGGACTCCAGGTTTTAGCACAAC -3'
Posted On 2014-09-18