Incidental Mutation 'PIT4531001:Sec24d'
ID 556445
Institutional Source Beutler Lab
Gene Symbol Sec24d
Ensembl Gene ENSMUSG00000039234
Gene Name SEC24 homolog D, COPII coat complex component
Synonyms LOC383951, 2310020L09Rik
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # PIT4531001 (G1)
Quality Score 225.009
Status Not validated
Chromosome 3
Chromosomal Location 123061104-123159290 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) C to T at 123136827 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Proline to Leucine at position 520 (P520L)
Ref Sequence ENSEMBL: ENSMUSP00000035823 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000047923]
AlphaFold Q6NXL1
Predicted Effect probably damaging
Transcript: ENSMUST00000047923
AA Change: P520L

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000035823
Gene: ENSMUSG00000039234
AA Change: P520L

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
Coding Region Coverage
  • 1x: 93.0%
  • 3x: 90.6%
  • 10x: 84.3%
  • 20x: 70.3%
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
Adpgk T G 9: 59,217,600 (GRCm39) D204E probably damaging Het
Aqr C A 2: 113,961,215 (GRCm39) V682L possibly damaging Het
Bmper A T 9: 23,136,113 (GRCm39) N65Y possibly damaging Het
Calb1 T C 4: 15,900,925 (GRCm39) L171P probably damaging Het
Card11 T C 5: 140,892,415 (GRCm39) M217V probably damaging Het
Col11a2 A G 17: 34,265,412 (GRCm39) probably null Het
Dpm1 T C 2: 168,052,472 (GRCm39) T255A probably benign Het
Efhb A G 17: 53,752,803 (GRCm39) Y440H probably damaging Het
Elp2 T C 18: 24,737,170 (GRCm39) V40A probably damaging Het
Far2 A T 6: 148,076,629 (GRCm39) N491Y possibly damaging Het
Frem1 T A 4: 82,868,517 (GRCm39) H1488L probably benign Het
Frrs1l C A 4: 56,990,144 (GRCm39) R43L unknown Het
Galnt3 G A 2: 65,937,432 (GRCm39) R93C probably benign Het
Gm8225 A G 17: 26,762,363 (GRCm39) T185A possibly damaging Het
H2-Q1 T C 17: 35,539,892 (GRCm39) F54L probably benign Het
H2-Q1 A T 17: 35,540,055 (GRCm39) Q108L probably damaging Het
Hoxc12 T G 15: 102,846,855 (GRCm39) L249W probably damaging Het
Lrrc75b A T 10: 75,393,099 (GRCm39) H83Q probably damaging Het
Muc4 A T 16: 32,576,391 (GRCm39) T1964S unknown Het
Nob1 T C 8: 108,145,049 (GRCm39) D142G probably benign Het
Or2y1d T C 11: 49,321,753 (GRCm39) V150A probably benign Het
Or4p19 A T 2: 88,242,104 (GRCm39) H299Q probably benign Het
Or4p22 A T 2: 88,317,601 (GRCm39) Y175F possibly damaging Het
Or5b24 G A 19: 12,912,641 (GRCm39) D180N probably damaging Het
Or5d16 A G 2: 87,773,571 (GRCm39) Y134H probably damaging Het
Patj A T 4: 98,329,327 (GRCm39) N527I probably damaging Het
Pik3c2g A G 6: 139,805,096 (GRCm39) I543V Het
Ppp1r2 A T 16: 31,077,279 (GRCm39) N150K probably damaging Het
Prl7d1 A T 13: 27,894,161 (GRCm39) L135Q probably damaging Het
Ralgds G T 2: 28,435,226 (GRCm39) E461* probably null Het
Ramac C T 7: 81,417,327 (GRCm39) P9L possibly damaging Het
Rasa3 T A 8: 13,655,887 (GRCm39) H116L probably benign Het
Sfmbt1 T G 14: 30,518,283 (GRCm39) S376A probably benign Het
Sspo A G 6: 48,458,173 (GRCm39) T3290A probably benign Het
Stk25 G A 1: 93,552,346 (GRCm39) P345S probably benign Het
Sycp2l A G 13: 41,300,148 (GRCm39) E454G probably null Het
Tecpr1 T C 5: 144,150,885 (GRCm39) K308E probably damaging Het
Thtpa C T 14: 55,332,962 (GRCm39) P16S probably damaging Het
Trim65 T A 11: 116,018,535 (GRCm39) I247F possibly damaging Het
Trpc6 T G 9: 8,610,149 (GRCm39) Y206D probably benign Het
Ttn G A 2: 76,703,307 (GRCm39) T9357I unknown Het
Ugt2b1 C A 5: 87,074,342 (GRCm39) A6S probably benign Het
Vmn1r175 A G 7: 23,508,603 (GRCm39) V8A possibly damaging Het
Vps13b T A 15: 35,878,971 (GRCm39) I2990N probably damaging Het
Xirp2 G A 2: 67,345,826 (GRCm39) R2689Q possibly damaging Het
Zfp831 T A 2: 174,488,516 (GRCm39) Y1064N 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
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
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'- AGCTCCTGCCTCAAGTTAGG -3'
(R):5'- ATGCTCATACAAGGAACAGGC -3'

Sequencing Primer
(F):5'- CCTGCCTCAAGTTAGGTTTTG -3'
(R):5'- AAGGAACAGGCCCCTTTCCTTC -3'
Posted On 2019-06-07