Incidental Mutation 'R0838:Sec24d'
ID 78029
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
MMRRC Submission 039017-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R0838 (G1)
Quality Score 225
Status Validated
Chromosome 3
Chromosomal Location 123061104-123159290 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 123099485 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Leucine at position 319 (F319L)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect probably benign
Transcript: ENSMUST00000047923
AA Change: F319L

PolyPhen 2 Score 0.076 (Sensitivity: 0.93; Specificity: 0.85)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: F319L

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: ENSMUST00000197291
Meta Mutation Damage Score 0.0640 question?
Coding Region Coverage
  • 1x: 99.4%
  • 3x: 98.7%
  • 10x: 97.2%
  • 20x: 94.3%
Validation Efficiency 100% (56/56)
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: 53 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2310057M21Rik T A 7: 130,963,535 (GRCm39) M53L probably damaging Het
Adamts6 A G 13: 104,550,297 (GRCm39) N638D possibly damaging Het
Amy2b T C 3: 113,058,317 (GRCm39) noncoding transcript Het
Ap5s1 G A 2: 131,053,351 (GRCm39) R45K probably damaging Het
Arap1 T C 7: 101,049,619 (GRCm39) Y994H probably damaging Het
Arrdc3 A T 13: 81,037,366 (GRCm39) probably benign Het
Bard1 G A 1: 71,069,812 (GRCm39) T722M probably damaging Het
Ccdc88a A G 11: 29,350,285 (GRCm39) Y89C probably damaging Het
Cd96 A G 16: 45,938,289 (GRCm39) S59P probably damaging Het
Chit1 T A 1: 134,071,075 (GRCm39) C51* probably null Het
Cilp2 G T 8: 70,334,369 (GRCm39) H876Q probably benign Het
Cyld A G 8: 89,467,978 (GRCm39) E722G probably benign Het
Dab1 C T 4: 104,588,948 (GRCm39) A524V probably benign Het
Dedd2 T C 7: 24,910,612 (GRCm39) E188G probably benign Het
Dnah17 A T 11: 117,950,930 (GRCm39) W2898R probably damaging Het
Dpy19l1 T C 9: 24,343,727 (GRCm39) T473A probably damaging Het
Fam228a T A 12: 4,785,002 (GRCm39) H43L possibly damaging Het
Fkbp15 G T 4: 62,242,363 (GRCm39) H530N probably damaging Het
Gga1 C T 15: 78,776,118 (GRCm39) S387L probably damaging Het
Gm4868 A G 5: 125,925,687 (GRCm39) noncoding transcript Het
Guk1 G A 11: 59,075,921 (GRCm39) R146C probably damaging Het
Itgb4 A C 11: 115,888,988 (GRCm39) probably benign Het
Jag1 G A 2: 136,935,198 (GRCm39) T388I probably damaging Het
Kcnh1 A G 1: 192,095,514 (GRCm39) D551G probably damaging Het
Lrp2bp A G 8: 46,478,161 (GRCm39) D270G possibly damaging Het
Map3k19 C A 1: 127,751,696 (GRCm39) V552F probably benign Het
Mixl1 A T 1: 180,524,365 (GRCm39) D71E probably benign Het
Myocd A G 11: 65,069,758 (GRCm39) I694T probably benign Het
Nadk2 T A 15: 9,091,322 (GRCm39) S198T probably benign Het
Npepps A T 11: 97,158,518 (GRCm39) probably benign Het
Nt5c1b C T 12: 10,425,071 (GRCm39) Q206* probably null Het
Or51b17 T A 7: 103,542,622 (GRCm39) I107F probably benign Het
Orm1 A G 4: 63,263,394 (GRCm39) Y69C probably damaging Het
Plscr4 T A 9: 92,353,813 (GRCm39) probably benign Het
Pon1 G A 6: 5,175,758 (GRCm39) T188I possibly damaging Het
Ppm1a T A 12: 72,831,094 (GRCm39) H206Q probably benign Het
Prl8a1 G A 13: 27,758,008 (GRCm39) R234C probably damaging Het
Rfx3 C T 19: 27,827,367 (GRCm39) R73Q possibly damaging Het
Rims2 T C 15: 39,544,421 (GRCm39) V1466A probably benign Het
Slc15a4 A G 5: 127,694,067 (GRCm39) S123P possibly damaging Het
Slc1a6 A T 10: 78,632,056 (GRCm39) D294V probably damaging Het
Slc28a3 A T 13: 58,736,083 (GRCm39) D38E probably benign Het
Spata31d1e A G 13: 59,890,282 (GRCm39) S513P possibly damaging Het
Stard3nl A G 13: 19,556,756 (GRCm39) probably null Het
Stard9 A G 2: 120,531,323 (GRCm39) T2527A probably damaging Het
Sult3a1 C T 10: 33,755,284 (GRCm39) P283L probably damaging Het
Tgtp1 A G 11: 48,877,970 (GRCm39) V245A probably benign Het
Txndc16 T C 14: 45,402,876 (GRCm39) probably benign Het
Zdhhc8 A G 16: 18,042,430 (GRCm39) L590S probably damaging Het
Zfp1005 T A 2: 150,111,220 (GRCm39) C637S possibly damaging Het
Zfp366 A G 13: 99,365,118 (GRCm39) E93G possibly damaging Het
Zfp69 T C 4: 120,788,478 (GRCm39) N279S probably benign Het
Zscan10 T C 17: 23,829,008 (GRCm39) S407P possibly 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
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
R4896:Sec24d UTSW 3 123,148,596 (GRCm39) missense probably damaging 1.00
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'- GCATGTCCCTGGAGTGTAGATCACAG -3'
(R):5'- AACTGGATACTTTCCTGGAGTTTGGC -3'

Sequencing Primer
(F):5'- GGAGTGTAGATCACAGAATTTTACAG -3'
(R):5'- ACTTTCCTGGAGTTTGGCATAAC -3'
Posted On 2013-10-16