Incidental Mutation 'R4896:Sec24d'
ID 434668
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
MMRRC Submission 042500-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R4896 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 123061104-123159290 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 123148596 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Cysteine to Arginine at position 747 (C747R)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect probably damaging
Transcript: ENSMUST00000047923
AA Change: C747R

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: C747R

DomainStartEndE-ValueType
low complexity region 46 71 N/A INTRINSIC
low complexity region 75 87 N/A INTRINSIC
low complexity region 136 160 N/A INTRINSIC
low complexity region 197 222 N/A INTRINSIC
low complexity region 238 256 N/A INTRINSIC
Pfam:zf-Sec23_Sec24 360 398 1.8e-16 PFAM
Pfam:Sec23_trunk 437 681 3.6e-88 PFAM
Pfam:Sec23_BS 686 770 2e-20 PFAM
Pfam:Sec23_helical 783 884 1e-27 PFAM
Pfam:Gelsolin 899 974 4.2e-12 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000196631
Predicted Effect noncoding transcript
Transcript: ENSMUST00000197291
Predicted Effect noncoding transcript
Transcript: ENSMUST00000200309
Meta Mutation Damage Score 0.9582 question?
Coding Region Coverage
  • 1x: 99.1%
  • 3x: 98.4%
  • 10x: 96.7%
  • 20x: 93.5%
Validation Efficiency 99% (101/102)
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 member of the SEC24 subfamily of the SEC23/SEC24 family, which is involved in vesicle trafficking. The encoded protein has similarity to yeast Sec24p component of COPII. COPII is the coat protein complex responsible for vesicle budding from the ER. This gene product is implicated in the shaping of the vesicle, and also in cargo selection and concentration. Mutations in this gene have been associated with Cole-Carpenter syndrome, a disorder affecting bone formation, resulting in craniofacial malformations and bones that break easily. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
PHENOTYPE: Mice homozygous for a knock-out allele exhibit early embryonic lethality. A hypomorphic gene trap allele results in lethality during organogenesis. [provided by MGI curators]
Allele List at MGI

All alleles(5) : Gene trapped(5)

Other mutations in this stock
Total: 95 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Abcb4 T C 5: 8,957,267 (GRCm39) V132A possibly damaging Het
Acp3 A T 9: 104,184,174 (GRCm39) V292E probably damaging Het
Adamts10 T C 17: 33,747,870 (GRCm39) V102A possibly damaging Het
Add2 A G 6: 86,073,728 (GRCm39) T206A probably benign Het
Alg12 A T 15: 88,700,391 (GRCm39) L15Q probably damaging Het
Ankrd27 T A 7: 35,307,800 (GRCm39) D346E probably damaging Het
Armc2 A T 10: 41,799,790 (GRCm39) N689K probably damaging Het
Best3 T A 10: 116,860,460 (GRCm39) D573E probably benign Het
Bltp1 T G 3: 37,020,086 (GRCm39) N2108K probably damaging Het
Ccdc80 A T 16: 44,916,261 (GRCm39) Q339L probably benign Het
Cdh9 T C 15: 16,778,242 (GRCm39) V19A probably benign Het
Cimap1a G A 7: 140,428,398 (GRCm39) probably benign Het
Cnksr1 A T 4: 133,956,986 (GRCm39) probably null Het
Col7a1 T A 9: 108,786,345 (GRCm39) V525E unknown Het
Cplane1 T C 15: 8,251,421 (GRCm39) S1898P probably benign Het
Crebrf T C 17: 26,961,394 (GRCm39) S172P possibly damaging Het
Csmd1 T C 8: 16,059,439 (GRCm39) I2099V probably benign Het
Dcaf4 T A 12: 83,586,233 (GRCm39) M400K possibly damaging Het
Dnah11 A T 12: 117,958,935 (GRCm39) F2983I probably damaging Het
Dock6 A G 9: 21,735,733 (GRCm39) V1005A possibly damaging Het
Dyrk2 C A 10: 118,704,153 (GRCm39) G34C probably damaging Het
Eif4a1 A T 11: 69,559,423 (GRCm39) probably benign Het
Eno4 G T 19: 58,952,975 (GRCm39) D330Y probably damaging Het
Faf1 G A 4: 109,699,496 (GRCm39) C347Y probably benign Het
Fam169a A G 13: 97,234,100 (GRCm39) Y124C probably damaging Het
Fam227a G T 15: 79,521,255 (GRCm39) F269L probably benign Het
Fancm C A 12: 65,122,605 (GRCm39) D42E probably damaging Het
Fat1 T A 8: 45,404,317 (GRCm39) I356N possibly damaging Het
Fer1l6 A T 15: 58,509,869 (GRCm39) T1444S probably damaging Het
Galr1 A G 18: 82,412,065 (GRCm39) L267P probably damaging Het
Gbx1 T C 5: 24,709,837 (GRCm39) H336R probably damaging Het
Gimap8 A T 6: 48,636,281 (GRCm39) Q682L possibly damaging Het
Gm2396 T G 9: 88,813,281 (GRCm39) noncoding transcript Het
Gm5798 T C 14: 41,070,614 (GRCm39) L8S probably damaging Het
Hmgcll1 C T 9: 75,963,460 (GRCm39) S39F possibly damaging Het
Hspg2 C T 4: 137,246,251 (GRCm39) R1010C probably damaging Het
Il3ra A T 14: 14,355,381 (GRCm38) E289D probably benign Het
Isoc1 T A 18: 58,806,350 (GRCm39) L220Q probably damaging Het
Itga2 T A 13: 114,990,302 (GRCm39) K918* probably null Het
Kat6a C T 8: 23,428,329 (GRCm39) T1228I probably benign Het
Klhl30 T A 1: 91,287,046 (GRCm39) probably null Het
Krtap6-2 A T 16: 89,216,806 (GRCm39) C54S unknown Het
Lmf2 G A 15: 89,236,003 (GRCm39) P634S probably benign Het
Map3k4 A G 17: 12,490,906 (GRCm39) V175A possibly damaging Het
Mcm3 A C 1: 20,890,480 (GRCm39) probably benign Het
Mon1b T C 8: 114,365,859 (GRCm39) S396P probably damaging Het
Mroh2a T C 1: 88,184,476 (GRCm39) V1453A probably benign Het
Ncor2 A G 5: 125,126,404 (GRCm39) probably null Het
Nlrc5 T G 8: 95,247,844 (GRCm39) probably benign Het
Nlrp14 GT GTT 7: 106,796,386 (GRCm39) probably null Het
Nwd2 T G 5: 63,962,151 (GRCm39) S578R probably damaging Het
Or12k7 A G 2: 36,958,422 (GRCm39) Y35C probably damaging Het
Or4f4b G A 2: 111,314,005 (GRCm39) V105I possibly damaging Het
Otoa C A 7: 120,701,902 (GRCm39) P194T probably damaging Het
Pde1b A C 15: 103,429,801 (GRCm39) D98A probably damaging Het
Pi4ka A T 16: 17,195,033 (GRCm39) C122S probably damaging Het
Pole2 C T 12: 69,269,924 (GRCm39) V67M probably damaging Het
Prickle2 A T 6: 92,393,736 (GRCm39) D312E probably benign Het
Prkd1 T C 12: 50,436,745 (GRCm39) D453G probably damaging Het
Prrc1 T A 18: 57,507,626 (GRCm39) V260E probably damaging Het
Reg3g A T 6: 78,444,793 (GRCm39) Y62N probably benign Het
Reln C T 5: 22,160,236 (GRCm39) G2111E probably damaging Het
Rsph6a A T 7: 18,791,665 (GRCm39) E278V possibly damaging Het
Scpep1 T A 11: 88,832,122 (GRCm39) I203F probably damaging Het
Sec31a A T 5: 100,516,192 (GRCm39) N967K probably damaging Het
Sell T C 1: 163,890,631 (GRCm39) W5R probably benign Het
Siglec1 C T 2: 130,911,789 (GRCm39) V1697M probably benign Het
Sinhcaf A G 6: 148,834,498 (GRCm39) probably null Het
Slc22a26 T A 19: 7,768,419 (GRCm39) I213L probably benign Het
Slc2a13 G A 15: 91,296,415 (GRCm39) P300S probably benign Het
Slco1a4 A G 6: 141,761,231 (GRCm39) Y461H possibly damaging Het
Slco3a1 G C 7: 73,970,304 (GRCm39) C434W probably null Het
Sp3 A T 2: 72,768,633 (GRCm39) V666D probably benign Het
Spidr A T 16: 15,936,806 (GRCm39) W100R possibly damaging Het
Stk33 T A 7: 108,926,802 (GRCm39) M286L probably damaging Het
Sult1c2 T A 17: 54,139,163 (GRCm39) I183F probably benign Het
Svep1 G T 4: 58,087,751 (GRCm39) T1776K probably benign Het
Tesk2 A G 4: 116,660,190 (GRCm39) H436R probably benign Het
Tex2 T C 11: 106,459,230 (GRCm39) T67A probably damaging Het
Timm10 T C 2: 84,660,192 (GRCm39) S44P possibly damaging Het
Tmed11 C A 5: 108,943,048 (GRCm39) probably null Het
Trim12c G A 7: 103,990,155 (GRCm39) R441C probably damaging Het
Trmt2a A G 16: 18,070,793 (GRCm39) K509E probably damaging Het
Upk3a A G 15: 84,903,624 (GRCm39) T108A probably benign Het
Usp29 A G 7: 6,965,158 (GRCm39) M334V probably benign Het
Vash1 A G 12: 86,726,916 (GRCm39) D52G probably benign Het
Vmn2r14 T G 5: 109,368,246 (GRCm39) T249P probably benign Het
Vmn2r43 A T 7: 8,247,848 (GRCm39) F772I probably damaging Het
Vmn2r75 G T 7: 85,820,787 (GRCm39) S49Y probably benign Het
Xdh T C 17: 74,217,238 (GRCm39) T677A probably damaging Het
Zan A G 5: 137,384,718 (GRCm39) L5102P unknown Het
Zfp160 T A 17: 21,240,343 (GRCm39) S9T probably benign Het
Zfp273 A T 13: 67,973,673 (GRCm39) H267L probably damaging Het
Zfp97 T A 17: 17,365,038 (GRCm39) I179K probably benign Het
Zfp975 T C 7: 42,311,716 (GRCm39) Y299C probably damaging Het
Other mutations in Sec24d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL01420:Sec24d APN 3 123,143,658 (GRCm39) missense probably benign 0.00
IGL01621:Sec24d APN 3 123,087,807 (GRCm39) critical splice acceptor site probably null
IGL01866:Sec24d APN 3 123,087,244 (GRCm39) nonsense probably null
IGL02064:Sec24d APN 3 123,137,463 (GRCm39) splice site probably benign
IGL02125:Sec24d APN 3 123,152,607 (GRCm39) missense probably damaging 1.00
IGL02173:Sec24d APN 3 123,147,330 (GRCm39) missense probably damaging 1.00
IGL03239:Sec24d APN 3 123,130,138 (GRCm39) missense probably benign 0.00
Scanty UTSW 3 123,148,596 (GRCm39) missense probably damaging 1.00
3-1:Sec24d UTSW 3 123,147,279 (GRCm39) missense possibly damaging 0.94
PIT4531001:Sec24d UTSW 3 123,136,827 (GRCm39) missense probably damaging 1.00
R0008:Sec24d UTSW 3 123,144,525 (GRCm39) splice site probably benign
R0838:Sec24d UTSW 3 123,099,485 (GRCm39) missense probably benign 0.08
R1775:Sec24d UTSW 3 123,130,166 (GRCm39) missense probably damaging 1.00
R1895:Sec24d UTSW 3 123,147,043 (GRCm39) missense probably benign 0.04
R1946:Sec24d UTSW 3 123,147,043 (GRCm39) missense probably benign 0.04
R2238:Sec24d UTSW 3 123,143,543 (GRCm39) splice site probably null
R2504:Sec24d UTSW 3 123,147,255 (GRCm39) missense possibly damaging 0.69
R2846:Sec24d UTSW 3 123,144,395 (GRCm39) missense probably damaging 0.98
R2895:Sec24d UTSW 3 123,136,800 (GRCm39) missense probably damaging 1.00
R3428:Sec24d UTSW 3 123,137,572 (GRCm39) splice site probably benign
R4573:Sec24d UTSW 3 123,152,519 (GRCm39) missense probably damaging 1.00
R4668:Sec24d UTSW 3 123,149,423 (GRCm39) missense probably damaging 0.98
R4706:Sec24d UTSW 3 123,149,427 (GRCm39) missense possibly damaging 0.80
R4982:Sec24d UTSW 3 123,093,255 (GRCm39) missense probably benign 0.29
R5030:Sec24d UTSW 3 123,152,550 (GRCm39) missense probably damaging 0.98
R5041:Sec24d UTSW 3 123,087,880 (GRCm39) missense probably damaging 0.96
R5078:Sec24d UTSW 3 123,084,201 (GRCm39) missense probably benign 0.00
R5108:Sec24d UTSW 3 123,099,434 (GRCm39) splice site probably null
R5174:Sec24d UTSW 3 123,158,575 (GRCm39) missense probably damaging 0.99
R5661:Sec24d UTSW 3 123,136,791 (GRCm39) missense possibly damaging 0.95
R5661:Sec24d UTSW 3 123,136,734 (GRCm39) missense probably damaging 1.00
R5775:Sec24d UTSW 3 123,084,109 (GRCm39) missense probably benign 0.00
R5859:Sec24d UTSW 3 123,072,961 (GRCm39) unclassified probably benign
R5944:Sec24d UTSW 3 123,087,230 (GRCm39) missense probably benign 0.01
R6053:Sec24d UTSW 3 123,072,871 (GRCm39) nonsense probably null
R6515:Sec24d UTSW 3 123,136,719 (GRCm39) missense possibly damaging 0.92
R6552:Sec24d UTSW 3 123,084,201 (GRCm39) missense probably benign 0.00
R6557:Sec24d UTSW 3 123,136,736 (GRCm39) missense probably damaging 1.00
R6593:Sec24d UTSW 3 123,147,061 (GRCm39) missense probably damaging 1.00
R6594:Sec24d UTSW 3 123,087,412 (GRCm39) missense probably damaging 1.00
R6842:Sec24d UTSW 3 123,136,868 (GRCm39) missense probably benign 0.00
R7072:Sec24d UTSW 3 123,124,000 (GRCm39) missense probably damaging 1.00
R7481:Sec24d UTSW 3 123,144,412 (GRCm39) missense probably damaging 1.00
R7554:Sec24d UTSW 3 123,149,423 (GRCm39) missense probably damaging 1.00
R8270:Sec24d UTSW 3 123,099,535 (GRCm39) missense possibly damaging 0.90
R8481:Sec24d UTSW 3 123,147,073 (GRCm39) missense probably damaging 1.00
R8713:Sec24d UTSW 3 123,137,541 (GRCm39) missense probably damaging 1.00
R8872:Sec24d UTSW 3 123,148,585 (GRCm39) splice site probably benign
R8922:Sec24d UTSW 3 123,144,488 (GRCm39) missense probably damaging 1.00
R8974:Sec24d UTSW 3 123,099,498 (GRCm39) missense probably damaging 1.00
R9015:Sec24d UTSW 3 123,121,287 (GRCm39) missense probably benign 0.43
R9050:Sec24d UTSW 3 123,144,374 (GRCm39) missense probably benign 0.00
R9065:Sec24d UTSW 3 123,149,452 (GRCm39) missense probably damaging 1.00
R9128:Sec24d UTSW 3 123,087,810 (GRCm39) missense probably benign
R9447:Sec24d UTSW 3 123,084,162 (GRCm39) missense probably benign 0.00
R9701:Sec24d UTSW 3 123,063,321 (GRCm39) missense probably damaging 1.00
R9758:Sec24d UTSW 3 123,136,803 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- GGCTTGATCGCTTAAACCATTG -3'
(R):5'- TAGCTACCCAATGAGTCTCAGC -3'

Sequencing Primer
(F):5'- TGTTACAGCGAATTAATTAGCCTTCC -3'
(R):5'- CTGACTCACCGAGCTATGAGATTAG -3'
Posted On 2016-10-24