Incidental Mutation 'R6552:Sec24d'
ID 521670
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
MMRRC Submission 044677-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R6552 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 123061104-123159290 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 123084201 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Isoleucine to Valine at position 127 (I127V)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect probably benign
Transcript: ENSMUST00000047923
AA Change: I127V

PolyPhen 2 Score 0.002 (Sensitivity: 0.99; Specificity: 0.30)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: I127V

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 0.0638 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.4%
  • 20x: 98.1%
Validation Efficiency
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: 46 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ang5 A T 14: 44,200,254 (GRCm39) H106L probably benign Het
Arsk A G 13: 76,220,315 (GRCm39) Y260H probably damaging Het
Atxn2l C T 7: 126,092,993 (GRCm39) V833M possibly damaging Het
Bpifa6 G A 2: 153,829,078 (GRCm39) D202N probably damaging Het
Ccdc103 A G 11: 102,774,970 (GRCm39) S190G probably benign Het
Col6a6 C T 9: 105,576,112 (GRCm39) V2083I probably damaging Het
Creb5 A G 6: 53,662,369 (GRCm39) D222G probably damaging Het
Cyp7a1 C T 4: 6,272,361 (GRCm39) W284* probably null Het
Dnmt3a T C 12: 3,957,623 (GRCm39) V868A probably damaging Het
Efr3a A G 15: 65,729,339 (GRCm39) D680G possibly damaging Het
Eml2 G A 7: 18,935,088 (GRCm39) V432I probably damaging Het
Epb41l4a A G 18: 34,012,032 (GRCm39) Y163H probably damaging Het
Gabra1 A T 11: 42,037,926 (GRCm39) S231T probably damaging Het
Golga4 T A 9: 118,343,299 (GRCm39) F42I probably damaging Het
Greb1l G A 18: 10,541,814 (GRCm39) S1187N probably benign Het
Haspin A G 11: 73,028,390 (GRCm39) V233A probably benign Het
Il34 T A 8: 111,469,059 (GRCm39) K187I probably benign Het
Kcnn2 A G 18: 45,693,165 (GRCm39) H247R probably benign Het
Klf5 T C 14: 99,539,078 (GRCm39) S84P probably benign Het
Lama5 G T 2: 179,822,947 (GRCm39) P2773Q probably damaging Het
Lcat T C 8: 106,666,311 (GRCm39) M404V possibly damaging Het
Lrp6 A T 6: 134,431,692 (GRCm39) S1473T probably benign Het
Lsm3 GATATATA GATATATATA 6: 91,496,617 (GRCm39) probably null Het
Mn1 T C 5: 111,568,753 (GRCm39) S908P possibly damaging Het
Or1o1 G A 17: 37,716,796 (GRCm39) R119H probably benign Het
Or2ag13 TGAAGCC T 7: 106,313,850 (GRCm39) probably benign Het
Pcdhb2 A T 18: 37,429,046 (GRCm39) M340L probably benign Het
Pex1 G A 5: 3,673,953 (GRCm39) E748K probably damaging Het
Qrich1 T C 9: 108,411,504 (GRCm39) V343A possibly damaging Het
Rho A G 6: 115,908,709 (GRCm39) probably null Het
Sdhaf4 C A 1: 24,044,687 (GRCm39) probably benign Het
Siae T C 9: 37,557,696 (GRCm39) V501A possibly damaging Het
Skint3 T C 4: 112,147,482 (GRCm39) Y402H possibly damaging Het
Skint6 A C 4: 112,924,687 (GRCm39) V515G possibly damaging Het
Slc23a1 C A 18: 35,755,391 (GRCm39) G475C probably damaging Het
Smad9 A G 3: 54,690,167 (GRCm39) Y129C probably damaging Het
Snw1 A G 12: 87,506,189 (GRCm39) probably null Het
Spice1 A G 16: 44,199,396 (GRCm39) D616G possibly damaging Het
Stam2 T C 2: 52,598,239 (GRCm39) probably null Het
Sumo3 G T 10: 77,442,091 (GRCm39) probably benign Het
Syne2 T G 12: 75,937,015 (GRCm39) N204K possibly damaging Het
Tmem200a T C 10: 25,869,381 (GRCm39) N296S probably damaging Het
Ttbk1 G T 17: 46,789,888 (GRCm39) T125N probably benign Het
Ubr2 G T 17: 47,277,194 (GRCm39) probably null Het
Vmn1r80 C T 7: 11,927,684 (GRCm39) L265F probably damaging Het
Vwa8 A T 14: 79,435,662 (GRCm39) T1791S 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
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
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'- CCACACAGAGGACTTGTTTTAGG -3'
(R):5'- TGGCATGCCCGAGTTATGTC -3'

Sequencing Primer
(F):5'- TGCTTAAGATGCTCAGTGATGCTATC -3'
(R):5'- CCTAGCACATCTACGGTT -3'
Posted On 2018-06-06