Incidental Mutation 'R0219:Necab3'
ID 33707
Institutional Source Beutler Lab
Gene Symbol Necab3
Ensembl Gene ENSMUSG00000027489
Gene Name N-terminal EF-hand calcium binding protein 3
Synonyms Apba2bp, XB51, 2900010M17Rik, Nip1
MMRRC Submission 038468-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.133) question?
Stock # R0219 (G1)
Quality Score 225
Status Validated
Chromosome 2
Chromosomal Location 154386319-154400810 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 154388013 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Lysine at position 292 (Q292K)
Ref Sequence ENSEMBL: ENSMUSP00000000895 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000000895] [ENSMUST00000045116] [ENSMUST00000109709] [ENSMUST00000109716] [ENSMUST00000125793]
AlphaFold Q9D6J4
Predicted Effect probably benign
Transcript: ENSMUST00000000895
AA Change: Q292K

PolyPhen 2 Score 0.170 (Sensitivity: 0.92; Specificity: 0.87)
SMART Domains Protein: ENSMUSP00000000895
Gene: ENSMUSG00000027489
AA Change: Q292K

DomainStartEndE-ValueType
Pfam:EF-hand_1 31 58 7.3e-8 PFAM
Pfam:EF-hand_5 32 57 4.6e-9 PFAM
low complexity region 180 203 N/A INTRINSIC
coiled coil region 209 237 N/A INTRINSIC
Pfam:ABM 252 327 4.4e-11 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000045116
SMART Domains Protein: ENSMUSP00000035523
Gene: ENSMUSG00000038523

DomainStartEndE-ValueType
Pfam:Bclt 1 194 2.1e-90 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000109709
SMART Domains Protein: ENSMUSP00000105331
Gene: ENSMUSG00000038523

DomainStartEndE-ValueType
Pfam:Bclt 1 207 1.9e-105 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000109716
AA Change: Q268K

PolyPhen 2 Score 0.141 (Sensitivity: 0.92; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000105338
Gene: ENSMUSG00000027489
AA Change: Q268K

DomainStartEndE-ValueType
Pfam:EF-hand_1 31 59 6.9e-8 PFAM
Pfam:EF-hand_5 32 57 1.7e-9 PFAM
low complexity region 180 203 N/A INTRINSIC
Pfam:ABM 232 303 2.7e-10 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000124382
Predicted Effect probably benign
Transcript: ENSMUST00000125793
SMART Domains Protein: ENSMUSP00000117090
Gene: ENSMUSG00000027489

DomainStartEndE-ValueType
low complexity region 146 168 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000135641
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130824
Meta Mutation Damage Score 0.0868 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 95.3%
Validation Efficiency 98% (65/66)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene interacts with the amino-terminal domain of the neuron-specific X11-like protein (X11L), inhibits the association of X11L with amyloid precursor protein through a non-competitive mechanism, and abolishes the suppression of beta-amyloid production by X11L. This protein, together with X11L, may play an important role in the regulatory system of amyloid precursor protein metabolism and beta-amyloid generation. The protein is phosphorylated by NIMA-related expressed kinase 2, and localizes to the Golgi apparatus. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 66 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb5 A T 12: 118,849,885 (GRCm39) probably benign Het
Acacb T A 5: 114,371,005 (GRCm39) M1749K possibly damaging Het
Aff1 GCTCTCTCTC GCTCTCTCTCTC 5: 103,958,906 (GRCm39) probably benign Het
Ankle2 C T 5: 110,399,511 (GRCm39) R624* probably null Het
Bcl2 G A 1: 106,640,292 (GRCm39) R107C probably damaging Het
Brca2 A G 5: 150,446,640 (GRCm39) probably benign Het
Ccdc116 T A 16: 16,959,476 (GRCm39) R404S possibly damaging Het
Ccdc171 A G 4: 83,614,678 (GRCm39) probably benign Het
Ccdc80 A G 16: 44,916,846 (GRCm39) K534R probably damaging Het
Ccna1 T C 3: 54,958,348 (GRCm39) I112V probably benign Het
Cdhr1 A C 14: 36,801,558 (GRCm39) L795R possibly damaging Het
Cilp C A 9: 65,176,872 (GRCm39) L43I possibly damaging Het
Dclk2 T C 3: 86,720,976 (GRCm39) probably benign Het
Ddx59 C A 1: 136,360,047 (GRCm39) probably benign Het
Dgkd T C 1: 87,865,996 (GRCm39) probably benign Het
Dicer1 A G 12: 104,658,384 (GRCm39) probably null Het
Dst T G 1: 34,342,559 (GRCm39) S5030A probably damaging Het
Dysf G A 6: 84,106,443 (GRCm39) probably benign Het
Farp1 C A 14: 121,481,012 (GRCm39) P471Q possibly damaging Het
Fbp2 A T 13: 63,001,862 (GRCm39) F118I probably damaging Het
Fcer1g A G 1: 171,058,795 (GRCm39) V31A possibly damaging Het
Glb1l2 A G 9: 26,717,618 (GRCm39) V21A probably benign Het
Gm9912 T C 3: 148,891,131 (GRCm39) I1V unknown Het
Guf1 G A 5: 69,716,929 (GRCm39) A164T probably damaging Het
Hbb-bs T C 7: 103,475,876 (GRCm39) H147R possibly damaging Het
Hnrnpr T A 4: 136,066,474 (GRCm39) probably benign Het
Iglon5 A T 7: 43,126,261 (GRCm39) V214E probably damaging Het
Isx C A 8: 75,616,589 (GRCm39) probably null Het
Kank4 T C 4: 98,666,702 (GRCm39) N582D probably benign Het
Kcp T A 6: 29,495,784 (GRCm39) R773W probably damaging Het
Kdm4c T C 4: 74,291,857 (GRCm39) C825R probably damaging Het
Krt25 G A 11: 99,208,885 (GRCm39) T315M probably benign Het
Lrp5 A T 19: 3,647,349 (GRCm39) S1298T probably damaging Het
Map3k10 T C 7: 27,356,156 (GRCm39) D921G probably damaging Het
Mrgprx1 C A 7: 47,671,294 (GRCm39) W151L probably damaging Het
Mylk3 T A 8: 86,081,873 (GRCm39) D375V probably damaging Het
Nav3 C T 10: 109,702,791 (GRCm39) probably null Het
Ncan A G 8: 70,567,984 (GRCm39) S43P probably benign Het
Nptx2 T C 5: 144,484,950 (GRCm39) S148P probably damaging Het
Or2at4 A T 7: 99,385,135 (GRCm39) I262L probably benign Het
Or6p1 G A 1: 174,258,032 (GRCm39) V13I probably benign Het
Pde6a A G 18: 61,419,006 (GRCm39) E794G possibly damaging Het
Pus7 T C 5: 23,980,964 (GRCm39) Y133C possibly damaging Het
Rad21l A G 2: 151,496,508 (GRCm39) probably benign Het
Rptor A T 11: 119,712,603 (GRCm39) probably benign Het
Sart1 C A 19: 5,438,424 (GRCm39) A78S probably benign Het
Shkbp1 T C 7: 27,051,486 (GRCm39) E191G probably benign Het
Slc6a18 A T 13: 73,822,751 (GRCm39) probably null Het
Stxbp5 T C 10: 9,646,272 (GRCm39) T147A probably benign Het
Sv2b A G 7: 74,807,015 (GRCm39) probably null Het
Syne2 A T 12: 76,088,778 (GRCm39) K5045N probably damaging Het
Tmem174 A C 13: 98,773,347 (GRCm39) M161R possibly damaging Het
Tmprss7 A G 16: 45,476,820 (GRCm39) V814A probably damaging Het
Togaram2 T C 17: 72,021,225 (GRCm39) probably benign Het
Tpr T C 1: 150,319,009 (GRCm39) probably null Het
Ttn T C 2: 76,730,572 (GRCm39) probably benign Het
Ubr4 T A 4: 139,157,568 (GRCm39) L2375Q possibly damaging Het
Utp20 T C 10: 88,600,537 (GRCm39) E1987G probably damaging Het
Utrn T C 10: 12,560,195 (GRCm39) T1365A probably damaging Het
Vmn2r116 T A 17: 23,605,072 (GRCm39) Y128* probably null Het
Vmn2r5 A G 3: 64,411,734 (GRCm39) V278A probably damaging Het
Vps13d C T 4: 144,832,479 (GRCm39) S2809N probably benign Het
Zfp212 G A 6: 47,903,619 (GRCm39) R68H probably damaging Het
Zfp442 A T 2: 150,253,160 (GRCm39) L33Q probably damaging Het
Zfp629 T C 7: 127,211,255 (GRCm39) S185G probably damaging Het
Zfp738 A G 13: 67,831,508 (GRCm39) probably benign Het
Other mutations in Necab3
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00090:Necab3 APN 2 154,389,488 (GRCm39) unclassified probably benign
IGL01515:Necab3 APN 2 154,396,611 (GRCm39) missense probably damaging 1.00
IGL02438:Necab3 APN 2 154,387,964 (GRCm39) missense probably damaging 1.00
IGL03150:Necab3 APN 2 154,396,662 (GRCm39) missense probably damaging 1.00
R0092:Necab3 UTSW 2 154,400,659 (GRCm39) missense possibly damaging 0.89
R0102:Necab3 UTSW 2 154,387,232 (GRCm39) missense probably damaging 1.00
R0102:Necab3 UTSW 2 154,387,232 (GRCm39) missense probably damaging 1.00
R0656:Necab3 UTSW 2 154,388,223 (GRCm39) missense probably null 0.28
R1728:Necab3 UTSW 2 154,388,795 (GRCm39) missense probably benign 0.09
R1729:Necab3 UTSW 2 154,388,795 (GRCm39) missense probably benign 0.09
R2192:Necab3 UTSW 2 154,388,999 (GRCm39) missense possibly damaging 0.62
R4622:Necab3 UTSW 2 154,397,502 (GRCm39) critical splice donor site probably null
R5434:Necab3 UTSW 2 154,389,379 (GRCm39) missense probably damaging 1.00
R5577:Necab3 UTSW 2 154,387,076 (GRCm39) splice site probably null
R6603:Necab3 UTSW 2 154,396,842 (GRCm39) missense probably damaging 1.00
R7792:Necab3 UTSW 2 154,388,200 (GRCm39) missense probably damaging 1.00
R8195:Necab3 UTSW 2 154,389,363 (GRCm39) missense probably benign 0.05
R8831:Necab3 UTSW 2 154,396,607 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- CTCGGCTACTGCCAGGACTAAATG -3'
(R):5'- TGCTGCTACATGAACTTCACAGGG -3'

Sequencing Primer
(F):5'- atcctcctgcctctgcc -3'
(R):5'- GGCCCAAAGCCATTGTCTG -3'
Posted On 2013-05-09