Incidental Mutation 'R5661:Sec24d'
ID 444076
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
MMRRC Submission 043304-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5661 (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 123136791 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Methionine to Threonine at position 508 (M508T)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect possibly damaging
Transcript: ENSMUST00000047923
AA Change: M508T

PolyPhen 2 Score 0.954 (Sensitivity: 0.79; Specificity: 0.95)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: M508T

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
Meta Mutation Damage Score 0.8922 question?
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.7%
  • 10x: 97.3%
  • 20x: 95.4%
Validation Efficiency 97% (57/59)
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
Actg2 A G 6: 83,497,754 (GRCm39) I166T probably damaging Het
Actn1 T C 12: 80,231,618 (GRCm39) E273G probably benign Het
Arhgap15 G A 2: 44,212,739 (GRCm39) R403H possibly damaging Het
Arhgef26 T C 3: 62,285,075 (GRCm39) probably benign Het
Avl9 A T 6: 56,702,087 (GRCm39) R81* probably null Het
Brd3 G A 2: 27,351,584 (GRCm39) T223I possibly damaging Het
Cacna2d4 T C 6: 119,320,492 (GRCm39) M890T probably benign Het
Carm1 A G 9: 21,498,295 (GRCm39) D433G probably benign Het
Ccdc40 A G 11: 119,128,753 (GRCm39) K427E probably benign Het
Ccdc80 T C 16: 44,947,808 (GRCm39) Y929H probably damaging Het
Ccr9 A C 9: 123,609,164 (GRCm39) Y282S probably benign Het
Det1 C T 7: 78,492,958 (GRCm39) E349K probably damaging Het
Enpep T A 3: 129,070,406 (GRCm39) N834Y probably damaging Het
Epha7 A T 4: 28,946,217 (GRCm39) probably null Het
Fap A T 2: 62,367,307 (GRCm39) probably benign Het
Foxn4 A G 5: 114,411,053 (GRCm39) C23R probably benign Het
Gad1-ps T C 10: 99,280,901 (GRCm39) noncoding transcript Het
Gli2 C A 1: 118,781,032 (GRCm39) E238* probably null Het
Gm20939 C A 17: 95,183,207 (GRCm39) H148N probably damaging Het
Gnl1 T C 17: 36,293,447 (GRCm39) Y211H probably benign Het
Gpat3 A T 5: 101,033,808 (GRCm39) K221* probably null Het
Hjurp G C 1: 88,204,937 (GRCm39) probably benign Het
Hnrnph1 A T 11: 50,275,507 (GRCm39) Q415L probably benign Het
Kansl3 T C 1: 36,388,038 (GRCm39) E383G possibly damaging Het
Kdm5b T C 1: 134,526,811 (GRCm39) V311A probably benign Het
Lipk T A 19: 34,009,727 (GRCm39) M215K probably benign Het
Madd A G 2: 90,984,778 (GRCm39) probably null Het
Meltf A G 16: 31,700,744 (GRCm39) E88G possibly damaging Het
Mis18bp1 A T 12: 65,195,626 (GRCm39) S713T probably benign Het
Mocos T A 18: 24,799,052 (GRCm39) probably null Het
Msto1 T A 3: 88,820,192 (GRCm39) D88V possibly damaging Het
Myo5a A G 9: 75,074,488 (GRCm39) Y799C probably benign Het
Nectin4 T A 1: 171,212,738 (GRCm39) L357H probably damaging Het
Or4p22 G A 2: 88,317,441 (GRCm39) V122M probably damaging Het
Or6c2 A T 10: 129,362,618 (GRCm39) H174L probably benign Het
Pax2 A G 19: 44,779,161 (GRCm39) N179S probably damaging Het
Pcdhac2 C A 18: 37,278,499 (GRCm39) T493K probably damaging Het
Pgk2 G T 17: 40,518,287 (GRCm39) C380* probably null Het
Pi4k2b G A 5: 52,900,906 (GRCm39) probably null Het
Plcb3 A G 19: 6,940,588 (GRCm39) V416A probably damaging Het
Pom121l2 G A 13: 22,168,425 (GRCm39) G899R possibly damaging Het
Ppp4r1 T C 17: 66,110,963 (GRCm39) probably null Het
Prkdc G A 16: 15,628,634 (GRCm39) E3460K possibly damaging Het
Psmb3 A G 11: 97,597,659 (GRCm39) E75G possibly damaging Het
Retnlb C T 16: 48,638,429 (GRCm39) T50I probably benign Het
Sec16a A G 2: 26,329,649 (GRCm39) S789P probably benign Het
Slc5a8 C T 10: 88,755,290 (GRCm39) L466F possibly damaging Het
Terf1 T A 1: 15,889,888 (GRCm39) V221E probably damaging Het
Trak1 A G 9: 121,272,703 (GRCm39) N187S possibly damaging Het
Trappc11 T A 8: 47,965,642 (GRCm39) D528V probably damaging Het
Tut4 A G 4: 108,370,384 (GRCm39) D761G probably benign Het
Vmn1r170 A G 7: 23,306,231 (GRCm39) N211S possibly damaging Het
Zfpm2 G A 15: 40,959,467 (GRCm39) W50* probably null 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
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 3 123,136,734 (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'- AGAAGCCTCATCTCGCTGGTAG -3'
(R):5'- TGCACTTGTAGTTGAACTGCAG -3'

Sequencing Primer
(F):5'- GCCTCATCTCGCTGGTAGAAAAATG -3'
(R):5'- GTTGAACTGCAGCACAATAGGTCTTC -3'
Posted On 2016-11-09