Incidental Mutation 'R5944:Sec24d'
ID 460467
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
MMRRC Submission 044136-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5944 (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 123087230 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Valine to Alanine at position 132 (V132A)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect probably benign
Transcript: ENSMUST00000047923
AA Change: V132A

PolyPhen 2 Score 0.008 (Sensitivity: 0.96; Specificity: 0.76)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: V132A

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 0.0898 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.6%
  • 10x: 97.9%
  • 20x: 93.8%
Validation Efficiency 86% (51/59)
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: 48 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acacb G T 5: 114,384,041 (GRCm39) R2190L probably damaging Het
Ankrd17 C T 5: 90,433,702 (GRCm39) R689H probably damaging Het
Apol7b A T 15: 77,307,967 (GRCm39) V176E probably damaging Het
Arsg T C 11: 109,426,137 (GRCm39) F319S probably damaging Het
Bcar3 T A 3: 122,316,932 (GRCm39) D634E probably benign Het
Bend7 T C 2: 4,749,167 (GRCm39) W95R probably damaging Het
Cenpj A G 14: 56,791,115 (GRCm39) probably null Het
Cfap91 G T 16: 38,148,672 (GRCm39) T252N probably damaging Het
Clasrp A T 7: 19,328,431 (GRCm39) Y116N probably damaging Het
Cldn17 T C 16: 88,303,597 (GRCm39) E44G probably damaging Het
Cyfip1 G A 7: 55,521,878 (GRCm39) E61K probably damaging Het
Dcaf13 A C 15: 39,010,072 (GRCm39) M419L probably benign Het
Eml4 A G 17: 83,753,472 (GRCm39) D269G possibly damaging Het
Fap T C 2: 62,372,605 (GRCm39) Y258C probably damaging Het
Fdxr T A 11: 115,160,672 (GRCm39) T288S probably benign Het
Frs3 T C 17: 48,003,233 (GRCm39) probably benign Het
Gm5581 T A 6: 131,145,363 (GRCm39) noncoding transcript Het
Gm7964 A G 7: 83,405,743 (GRCm39) D187G probably benign Het
Gpc5 T C 14: 115,607,250 (GRCm39) V284A probably benign Het
Hspa9 T C 18: 35,082,076 (GRCm39) T177A possibly damaging Het
Ifi202b T A 1: 173,791,365 (GRCm39) M438L probably benign Het
Ighv1-3 T C 12: 114,445,239 (GRCm39) probably benign Het
Krt36 G T 11: 99,996,139 (GRCm39) A95E probably benign Het
Krt9 C T 11: 100,079,265 (GRCm39) S709N unknown Het
Lmntd1 A T 6: 145,373,042 (GRCm39) S164T probably damaging Het
Or14c41 T A 7: 86,234,486 (GRCm39) M1K probably null Het
Or2ag1b A T 7: 106,288,853 (GRCm39) C28* probably null Het
Or52n4b G A 7: 108,144,484 (GRCm39) A249T possibly damaging Het
Or5b94 C T 19: 12,652,283 (GRCm39) T238I probably damaging Het
Or7a41 A T 10: 78,871,223 (GRCm39) M198L probably benign Het
Papola T A 12: 105,778,644 (GRCm39) F341I possibly damaging Het
Phf3 A G 1: 30,859,785 (GRCm39) L914P probably damaging Het
Serpini1 G A 3: 75,547,606 (GRCm39) D373N probably damaging Het
Sigirr T C 7: 140,671,300 (GRCm39) Y394C probably damaging Het
Slc29a4 G A 5: 142,704,573 (GRCm39) E372K probably damaging Het
Slc7a4 C T 16: 17,392,220 (GRCm39) V405I possibly damaging Het
Spatc1 T C 15: 76,168,138 (GRCm39) L199P probably damaging Het
Srgap3 T C 6: 112,772,775 (GRCm39) M149V possibly damaging Het
Srsf11 C T 3: 157,728,981 (GRCm39) probably benign Het
Stat3 C T 11: 100,785,931 (GRCm39) A449T probably damaging Het
Stat4 A G 1: 52,113,898 (GRCm39) N203D probably damaging Het
Tanc1 T C 2: 59,667,564 (GRCm39) probably null Het
Trav3-1 T C 14: 52,818,449 (GRCm39) I41T probably benign Het
Usp34 T A 11: 23,313,089 (GRCm39) D525E probably damaging Het
Vars1 T C 17: 35,232,620 (GRCm39) V848A probably damaging Het
Vmn2r101 A T 17: 19,809,769 (GRCm39) D185V probably benign Het
Wiz A G 17: 32,576,671 (GRCm39) S628P probably benign Het
Zfp647 G A 15: 76,796,285 (GRCm39) P125L 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
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
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'- GATCACATAAGGTTAATGCACTTGG -3'
(R):5'- GCCATCTTGCCTGTGAGTTG -3'

Sequencing Primer
(F):5'- TGAAGCCAAGTTCGGTTACC -3'
(R):5'- CCTGTGAGTTGGTGGAGACATAG -3'
Posted On 2017-02-28