Incidental Mutation 'R3418:Clec9a'
ID 266894
Institutional Source Beutler Lab
Gene Symbol Clec9a
Ensembl Gene ENSMUSG00000046080
Gene Name C-type lectin domain family 9, member a
Synonyms DNGR-1, 9830005G06Rik
MMRRC Submission 040636-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R3418 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 129385825-129401726 bp(+) (GRCm39)
Type of Mutation intron
DNA Base Change (assembly) A to G at 129398001 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change
Ref Sequence ENSEMBL: ENSMUSP00000144990 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000058352] [ENSMUST00000088075] [ENSMUST00000164513] [ENSMUST00000203162] [ENSMUST00000204860]
AlphaFold Q8BRU4
Predicted Effect probably benign
Transcript: ENSMUST00000058352
SMART Domains Protein: ENSMUSP00000056625
Gene: ENSMUSG00000046080

DomainStartEndE-ValueType
transmembrane domain 32 54 N/A INTRINSIC
CLECT 137 256 8.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000088075
SMART Domains Protein: ENSMUSP00000085394
Gene: ENSMUSG00000046080

DomainStartEndE-ValueType
transmembrane domain 32 54 N/A INTRINSIC
CLECT 111 230 8.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000164513
SMART Domains Protein: ENSMUSP00000128622
Gene: ENSMUSG00000046080

DomainStartEndE-ValueType
CLECT 110 229 8.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000203162
SMART Domains Protein: ENSMUSP00000144896
Gene: ENSMUSG00000033082

DomainStartEndE-ValueType
Blast:CLECT 1 48 1e-23 BLAST
transmembrane domain 50 72 N/A INTRINSIC
coiled coil region 82 120 N/A INTRINSIC
CLECT 136 205 5.1e-2 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000203592
Predicted Effect probably benign
Transcript: ENSMUST00000204860
SMART Domains Protein: ENSMUSP00000144990
Gene: ENSMUSG00000046080

DomainStartEndE-ValueType
transmembrane domain 32 54 N/A INTRINSIC
Meta Mutation Damage Score 0.0898 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.2%
  • 20x: 94.6%
Validation Efficiency 98% (61/62)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] CLEC9A is a group V C-type lectin-like receptor (CTLR) that functions as an activation receptor and is expressed on myeloid lineage cells (Huysamen et al., 2008 [PubMed 18408006]).[supplied by OMIM, Aug 2008]
PHENOTYPE: Homozygous null mice have CD8alpha+ dendritic cells that are defective in cross-presentation of dead-cell associated antigens. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 60 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
5530400C23Rik A G 6: 133,271,082 (GRCm39) Q42R probably benign Het
Acaa1a A G 9: 119,178,556 (GRCm39) probably null Het
Agbl5 T C 5: 31,062,067 (GRCm39) S756P probably damaging Het
Armc9 T C 1: 86,122,060 (GRCm39) L395P probably damaging Het
Cdc16 C T 8: 13,819,489 (GRCm39) Q362* probably null Het
Cdh5 C T 8: 104,856,002 (GRCm39) R312C probably damaging Het
Cep170b C T 12: 112,704,902 (GRCm39) Q887* probably null Het
Chd9 T C 8: 91,763,219 (GRCm39) I2348T probably damaging Het
Col6a3 T C 1: 90,731,813 (GRCm39) D873G probably benign Het
D130040H23Rik T C 8: 69,755,579 (GRCm39) I328T probably benign Het
Dido1 G T 2: 180,302,728 (GRCm39) D1725E possibly damaging Het
Dnajb14 A G 3: 137,598,631 (GRCm39) D123G probably null Het
Dock2 A T 11: 34,580,587 (GRCm39) M661K probably damaging Het
Esam C T 9: 37,448,426 (GRCm39) probably null Het
Fam20c A T 5: 138,743,623 (GRCm39) N220Y probably damaging Het
Fat2 G T 11: 55,169,824 (GRCm39) H2978Q probably benign Het
Fbn1 T C 2: 125,162,846 (GRCm39) T2147A possibly damaging Het
Fdft1 T C 14: 63,394,070 (GRCm39) T214A probably damaging Het
Fhl5 T C 4: 25,211,252 (GRCm39) S147G probably benign Het
Flrt2 A G 12: 95,747,378 (GRCm39) Y572C probably damaging Het
Gcat A T 15: 78,926,297 (GRCm39) T56S possibly damaging Het
Gemin5 A T 11: 58,047,454 (GRCm39) probably null Het
Gm4736 A T 6: 132,092,640 (GRCm39) noncoding transcript Het
Grin2b T C 6: 135,820,108 (GRCm39) N368S probably benign Het
Gsto1 T C 19: 47,846,344 (GRCm39) F64L probably benign Het
Gucy1a1 A G 3: 82,013,440 (GRCm39) S401P probably damaging Het
Htr1f G A 16: 64,746,260 (GRCm39) P344L probably damaging Het
Ighv7-3 T A 12: 114,116,919 (GRCm39) Y81F probably damaging Het
Jakmip3 C A 7: 138,619,474 (GRCm39) probably benign Het
Kcnj13 T C 1: 87,314,641 (GRCm39) T194A probably benign Het
Khdrbs3 T C 15: 68,921,224 (GRCm39) probably benign Het
Klk14 G A 7: 43,341,501 (GRCm39) C51Y probably damaging Het
Lyn A T 4: 3,746,833 (GRCm39) I204F probably damaging Het
Mbd6 C G 10: 127,122,372 (GRCm39) R152P probably null Het
Myof A G 19: 37,911,426 (GRCm39) S1502P probably damaging Het
Myom2 T G 8: 15,135,294 (GRCm39) I499S probably benign Het
Nos2 T A 11: 78,850,521 (GRCm39) F1126L possibly damaging Het
Or3a4 G A 11: 73,944,814 (GRCm39) T257I probably damaging Het
P2ry1 T C 3: 60,911,133 (GRCm39) F91L probably damaging Het
Pcdh15 C A 10: 74,420,054 (GRCm39) D1166E probably benign Het
Pou6f1 C A 15: 100,478,805 (GRCm39) V368L probably benign Het
Ptcd3 A T 6: 71,860,470 (GRCm39) I579K possibly damaging Het
Rbm45 A G 2: 76,209,362 (GRCm39) E392G probably damaging Het
Rnf168 A G 16: 32,118,010 (GRCm39) N524D probably benign Het
Rnf222 G T 11: 68,783,982 (GRCm39) R183L probably damaging Het
Robo1 C T 16: 72,832,805 (GRCm39) T1526I probably benign Het
Sel1l A G 12: 91,776,776 (GRCm39) W689R probably damaging Het
Serpinb13 T C 1: 106,926,657 (GRCm39) S218P probably damaging Het
Serpini1 A G 3: 75,547,589 (GRCm39) Y367C probably damaging Het
Slc13a2 A G 11: 78,291,666 (GRCm39) F329S probably benign Het
Smc2 T C 4: 52,476,850 (GRCm39) probably benign Het
Sycp2 A T 2: 178,043,446 (GRCm39) probably benign Het
Tab2 G A 10: 7,783,245 (GRCm39) P679L probably damaging Het
Tdrd1 T A 19: 56,819,663 (GRCm39) N54K possibly damaging Het
Tgfbr2 T C 9: 115,958,901 (GRCm39) Y146C probably damaging Het
Tnfrsf11a A G 1: 105,737,130 (GRCm39) D79G possibly damaging Het
Trpa1 T C 1: 14,944,605 (GRCm39) I1046M probably benign Het
Ubn1 A G 16: 4,892,243 (GRCm39) probably benign Het
Ubp1 T C 9: 113,780,754 (GRCm39) probably null Het
Vmn2r2 A T 3: 64,024,320 (GRCm39) F754I probably benign Het
Other mutations in Clec9a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01676:Clec9a APN 6 129,398,118 (GRCm39) missense probably benign 0.35
PIT4468001:Clec9a UTSW 6 129,396,597 (GRCm39) critical splice donor site probably null
R0408:Clec9a UTSW 6 129,396,532 (GRCm39) missense possibly damaging 0.87
R1131:Clec9a UTSW 6 129,387,278 (GRCm39) missense probably damaging 1.00
R1888:Clec9a UTSW 6 129,387,249 (GRCm39) missense probably benign
R1888:Clec9a UTSW 6 129,387,249 (GRCm39) missense probably benign
R2085:Clec9a UTSW 6 129,387,274 (GRCm39) missense probably benign 0.07
R2095:Clec9a UTSW 6 129,393,321 (GRCm39) missense possibly damaging 0.84
R4731:Clec9a UTSW 6 129,393,299 (GRCm39) missense probably benign 0.13
R6547:Clec9a UTSW 6 129,393,339 (GRCm39) missense probably benign 0.01
R7728:Clec9a UTSW 6 129,392,198 (GRCm39) missense possibly damaging 0.93
R8078:Clec9a UTSW 6 129,385,996 (GRCm39) missense probably benign 0.44
R8349:Clec9a UTSW 6 129,387,292 (GRCm39) missense probably damaging 0.96
R8449:Clec9a UTSW 6 129,387,292 (GRCm39) missense probably damaging 0.96
R9050:Clec9a UTSW 6 129,396,561 (GRCm39) missense possibly damaging 0.86
R9476:Clec9a UTSW 6 129,398,023 (GRCm39) missense possibly damaging 0.92
R9510:Clec9a UTSW 6 129,398,023 (GRCm39) missense possibly damaging 0.92
Predicted Primers PCR Primer
(F):5'- GCTATTGATGGTGAAGGGCC -3'
(R):5'- AGTATCAGGCTTCTTTGTCTGC -3'

Sequencing Primer
(F):5'- TAAAAGAATCGTGTGCATGTGTG -3'
(R):5'- CTTCTTTGTCTGCTGGAGAAAAC -3'
Posted On 2015-02-18