Incidental Mutation 'R8078:Clec9a'
ID 629144
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 067512-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R8078 (G1)
Quality Score 225.009
Status Validated
Chromosome 6
Chromosomal Location 129385825-129401726 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 129385996 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Serine to Glycine at position 27 (S27G)
Ref Sequence ENSEMBL: ENSMUSP00000056625 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000032262] [ENSMUST00000058352] [ENSMUST00000088075] [ENSMUST00000112079] [ENSMUST00000112081] [ENSMUST00000164513] [ENSMUST00000204860]
AlphaFold Q8BRU4
Predicted Effect probably benign
Transcript: ENSMUST00000032262
SMART Domains Protein: ENSMUSP00000032262
Gene: ENSMUSG00000030159

DomainStartEndE-ValueType
transmembrane domain 28 50 N/A INTRINSIC
CLECT 102 217 1.59e-18 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000058352
AA Change: S27G

PolyPhen 2 Score 0.439 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000056625
Gene: ENSMUSG00000046080
AA Change: S27G

DomainStartEndE-ValueType
transmembrane domain 32 54 N/A INTRINSIC
CLECT 137 256 8.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000088075
AA Change: S27G

PolyPhen 2 Score 0.043 (Sensitivity: 0.94; Specificity: 0.83)
SMART Domains Protein: ENSMUSP00000085394
Gene: ENSMUSG00000046080
AA Change: S27G

DomainStartEndE-ValueType
transmembrane domain 32 54 N/A INTRINSIC
CLECT 111 230 8.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000112079
Predicted Effect probably benign
Transcript: ENSMUST00000112081
SMART Domains Protein: ENSMUSP00000107712
Gene: ENSMUSG00000030159

DomainStartEndE-ValueType
CLECT 70 185 1.59e-18 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000164513
AA Change: S27G

PolyPhen 2 Score 0.182 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000128622
Gene: ENSMUSG00000046080
AA Change: S27G

DomainStartEndE-ValueType
CLECT 110 229 8.6e-24 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000204860
AA Change: S27G

PolyPhen 2 Score 0.207 (Sensitivity: 0.92; Specificity: 0.88)
SMART Domains Protein: ENSMUSP00000144990
Gene: ENSMUSG00000046080
AA Change: S27G

DomainStartEndE-ValueType
transmembrane domain 32 54 N/A INTRINSIC
Meta Mutation Damage Score 0.0846 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.7%
  • 10x: 98.8%
  • 20x: 95.9%
Validation Efficiency 100% (63/63)
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abca13 G A 11: 9,251,279 (GRCm39) V2884I probably benign Het
Actl10 T A 2: 154,394,490 (GRCm39) N147K probably benign Het
Agpat2 C A 2: 26,494,113 (GRCm39) C37F possibly damaging Het
Alb G C 5: 90,615,214 (GRCm39) R242P probably damaging Het
Ankrd26 T A 6: 118,494,854 (GRCm39) probably null Het
Bcas1 T C 2: 170,260,532 (GRCm39) E49G possibly damaging Het
Birc2 A G 9: 7,858,742 (GRCm39) V331A probably damaging Het
Cadm3 A G 1: 173,168,626 (GRCm39) V314A probably damaging Het
Cep290 T C 10: 100,408,749 (GRCm39) V2407A probably benign Het
Chd5 C A 4: 152,445,448 (GRCm39) N446K possibly damaging Het
Coro1c G T 5: 114,020,164 (GRCm39) A17E probably damaging Het
Cspg4 T C 9: 56,797,543 (GRCm39) S1336P possibly damaging Het
Ddx55 G A 5: 124,704,451 (GRCm39) V353M probably damaging Het
Farp1 T A 14: 121,513,712 (GRCm39) S836T probably benign Het
Fbll1 G T 11: 35,688,728 (GRCm39) D178E probably benign Het
Flg2 T G 3: 93,107,582 (GRCm39) D22E probably damaging Het
Glis1 T A 4: 107,425,099 (GRCm39) C237S probably damaging Het
Gm5519 T C 19: 33,800,357 (GRCm39) V17A possibly damaging Het
Gucy2c C A 6: 136,674,919 (GRCm39) G1055C probably damaging Het
Hspg2 T C 4: 137,235,333 (GRCm39) Y123H probably damaging Het
Idh1 T A 1: 65,200,225 (GRCm39) I380F probably damaging Het
Il23r A T 6: 67,400,577 (GRCm39) N584K probably damaging Het
Irag1 T C 7: 110,498,942 (GRCm39) E363G probably damaging Het
Lama1 A T 17: 68,098,289 (GRCm39) T1829S Het
Ldlrad1 G A 4: 107,066,688 (GRCm39) A8T probably benign Het
Luzp2 T A 7: 54,702,510 (GRCm39) Y24* probably null Het
Masp2 A T 4: 148,698,235 (GRCm39) T439S probably benign Het
Meioc G A 11: 102,559,226 (GRCm39) W49* probably null Het
Mtor T G 4: 148,552,744 (GRCm39) I749S probably benign Het
Myo16 T A 8: 10,612,078 (GRCm39) V1241D unknown Het
Ncam2 G T 16: 81,240,136 (GRCm39) R199L possibly damaging Het
Nyap2 A G 1: 81,218,772 (GRCm39) S265G possibly damaging Het
Or4f15 T A 2: 111,813,615 (GRCm39) D268V probably damaging Het
Parp8 A T 13: 117,061,519 (GRCm39) F175I probably damaging Het
Pcnx1 A G 12: 82,022,054 (GRCm39) T823A Het
Phc2 T A 4: 128,604,855 (GRCm39) I197N probably damaging Het
Plaat3 C T 19: 7,556,526 (GRCm39) T109I probably benign Het
Pot1a T C 6: 25,750,107 (GRCm39) I518M probably benign Het
Prg2 T A 2: 84,812,604 (GRCm39) C105S probably benign Het
Rab39 A G 9: 53,617,255 (GRCm39) L54P possibly damaging Het
Rell1 T A 5: 64,097,064 (GRCm39) probably benign Het
Repin1 G T 6: 48,574,279 (GRCm39) E403* probably null Het
Slc4a4 T C 5: 89,327,566 (GRCm39) Y668H probably benign Het
Sncg C A 14: 34,096,727 (GRCm39) probably benign Het
Spata31d1b A G 13: 59,863,263 (GRCm39) D137G probably damaging Het
Tas1r1 C T 4: 152,112,803 (GRCm39) G750D probably damaging Het
Tcea3 A T 4: 135,981,825 (GRCm39) D61V probably damaging Het
Tfap2c T A 2: 172,393,392 (GRCm39) H102Q probably damaging Het
Tmem150a T A 6: 72,335,306 (GRCm39) L95H probably damaging Het
Tnfrsf11a A T 1: 105,745,409 (GRCm39) D149V probably damaging Het
Tsc22d2 C A 3: 58,323,453 (GRCm39) A115E probably benign Het
Vmn2r101 T A 17: 19,810,507 (GRCm39) F431Y probably benign Het
Vmn2r111 T C 17: 22,778,032 (GRCm39) N549S possibly damaging Het
Vmn2r85 C A 10: 130,265,364 (GRCm39) E40* probably null Het
Zfp606 G A 7: 12,214,942 (GRCm39) A57T possibly damaging Het
Zfp760 T C 17: 21,942,436 (GRCm39) V537A 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
R3418:Clec9a UTSW 6 129,398,001 (GRCm39) intron probably benign
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
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'- ATGAACATCCTTTAATCCCTGTTGC -3'
(R):5'- CTGATCTGAGTGCCCTTCAC -3'

Sequencing Primer
(F):5'- CTGTGAAAAAGTAGCCAGTTCC -3'
(R):5'- ACTTACTCCTCCATGCTGACGAATG -3'
Posted On 2020-06-30