Incidental Mutation 'R8270:Sec24d'
ID 639431
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
MMRRC Submission 067694-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R8270 (G1)
Quality Score 225.009
Status Validated
Chromosome 3
Chromosomal Location 123061104-123159290 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 123099535 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 336 (V336A)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect possibly damaging
Transcript: ENSMUST00000047923
AA Change: V336A

PolyPhen 2 Score 0.900 (Sensitivity: 0.82; Specificity: 0.94)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: V336A

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
Meta Mutation Damage Score 0.2152 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 100.0%
  • 10x: 99.9%
  • 20x: 99.6%
Validation Efficiency 98% (52/53)
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: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Adgrv1 G A 13: 81,651,163 (GRCm39) T3044I probably damaging Het
Apbb1ip C T 2: 22,765,004 (GRCm39) P562S unknown Het
Arhgap44 A G 11: 64,912,860 (GRCm39) M477T possibly damaging Het
Arhgef12 T C 9: 42,882,354 (GRCm39) T1497A probably benign Het
Atp5pd T C 11: 115,307,698 (GRCm39) D91G probably damaging Het
Atp6v0a4 A G 6: 38,051,164 (GRCm39) F405L probably damaging Het
Bicc1 T A 10: 70,767,938 (GRCm39) T893S probably damaging Het
Cacna1i T A 15: 80,257,835 (GRCm39) C1122S probably damaging Het
Capn7 A G 14: 31,080,636 (GRCm39) E369G probably damaging Het
Cass4 T A 2: 172,269,589 (GRCm39) L557Q probably damaging Het
Cdh5 A G 8: 104,839,672 (GRCm39) I48V probably benign Het
Crisp3 T C 17: 40,546,813 (GRCm39) K35R probably benign Het
Csde1 G A 3: 102,946,071 (GRCm39) A22T possibly damaging Het
Ctse T C 1: 131,595,877 (GRCm39) Y190H probably damaging Het
Cyp2d34 T A 15: 82,504,988 (GRCm39) D24V possibly damaging Het
D630045J12Rik A T 6: 38,167,658 (GRCm39) Y981* probably null Het
Dclre1a G A 19: 56,533,382 (GRCm39) T404I possibly damaging Het
Dmc1 T C 15: 79,485,746 (GRCm39) D23G probably damaging Het
Dnah8 C T 17: 31,059,687 (GRCm39) T4429M probably damaging Het
Esf1 A T 2: 139,997,033 (GRCm39) probably benign Het
Fbxl12 C A 9: 20,550,160 (GRCm39) R165L possibly damaging Het
Fn3k A T 11: 121,330,137 (GRCm39) M107L probably benign Het
Fxyd5 A G 7: 30,740,854 (GRCm39) L10P probably damaging Het
Gm21958 G A 3: 54,621,633 (GRCm39) probably benign Het
Gm4922 C T 10: 18,659,760 (GRCm39) D321N probably benign Het
Gtf2h3 A G 5: 124,734,050 (GRCm39) *310W probably null Het
Hapln2 G A 3: 87,930,851 (GRCm39) T180I possibly damaging Het
Herc1 T G 9: 66,395,232 (GRCm39) V4189G probably damaging Het
Iqgap1 A G 7: 80,379,875 (GRCm39) V1166A probably damaging Het
Kcnk10 T C 12: 98,401,358 (GRCm39) N439S Het
Klhl3 A T 13: 58,260,968 (GRCm39) M15K Het
Klk1b26 A T 7: 43,665,544 (GRCm39) T151S probably benign Het
Krtap5-1 C A 7: 141,850,199 (GRCm39) C176F unknown Het
Krtap5-3 T A 7: 141,755,693 (GRCm39) C177S unknown Het
Lrrc37 T C 11: 103,434,141 (GRCm39) I3009M unknown Het
Map1a T C 2: 121,129,501 (GRCm39) F180L probably damaging Het
Mfap5 T C 6: 122,498,889 (GRCm39) probably null Het
Nckap1 T A 2: 80,355,008 (GRCm39) H638L possibly damaging Het
Optc C T 1: 133,832,810 (GRCm39) V97M probably benign Het
Or5p78 T A 7: 108,212,150 (GRCm39) I212N probably benign Het
Or8b46 T G 9: 38,450,644 (GRCm39) M151R noncoding transcript Het
Piezo1 A G 8: 123,228,298 (GRCm39) Y330H Het
Ppp1r12b G T 1: 134,803,886 (GRCm39) N424K probably benign Het
Prdm5 T A 6: 65,913,058 (GRCm39) F580L probably damaging Het
Prr27 A C 5: 87,994,171 (GRCm39) K348N possibly damaging Het
Prr30 A G 14: 101,435,822 (GRCm39) Y247H possibly damaging Het
Rbks A T 5: 31,807,810 (GRCm39) probably benign Het
Serac1 A T 17: 6,101,033 (GRCm39) L457H probably damaging Het
Serpina1f A G 12: 103,659,757 (GRCm39) I175T probably damaging Het
Smr2l T C 5: 88,430,383 (GRCm39) V93A possibly damaging Het
Sspo A T 6: 48,426,897 (GRCm39) H242L probably benign Het
Tcaf2 A T 6: 42,606,958 (GRCm39) M332K probably benign Het
Tnrc6a T A 7: 122,769,294 (GRCm39) N361K possibly damaging Het
Trim43b G T 9: 88,967,458 (GRCm39) H393N possibly damaging Het
Ush2a T C 1: 188,176,838 (GRCm39) L1334S probably benign Het
Usp35 T C 7: 96,961,551 (GRCm39) E625G probably benign 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 3 123,136,791 (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
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'- CATGTCCCTGGAGTGTAGATC -3'
(R):5'- AGACGGATTGCTTGACCAGG -3'

Sequencing Primer
(F):5'- GGATGGATTGTTTAGATGTACCTTTG -3'
(R):5'- CGGATTGCTTGACCAGGTATTTTTAC -3'
Posted On 2020-07-28