Incidental Mutation 'R6475:Sec31a'
ID 517368
Institutional Source Beutler Lab
Gene Symbol Sec31a
Ensembl Gene ENSMUSG00000035325
Gene Name SEC31 homolog A, COPII coat complex component
Synonyms 1810024J13Rik, Sec31l1
MMRRC Submission 044608-MU
Accession Numbers
Essential gene? Probably essential (E-score: 0.855) question?
Stock # R6475 (G1)
Quality Score 225.009
Status Validated
Chromosome 5
Chromosomal Location 100509508-100564093 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 100533129 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 539 (T539A)
Ref Sequence ENSEMBL: ENSMUSP00000138213 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000094578] [ENSMUST00000182886] [ENSMUST00000183247]
AlphaFold Q3UPL0
Predicted Effect probably damaging
Transcript: ENSMUST00000094578
AA Change: T578A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000092157
Gene: ENSMUSG00000035325
AA Change: T578A

DomainStartEndE-ValueType
WD40 56 102 1.59e1 SMART
WD40 111 151 5.15e-2 SMART
WD40 158 197 5.16e-1 SMART
WD40 200 245 6.63e0 SMART
WD40 249 289 1.95e-2 SMART
WD40 292 332 4.24e-3 SMART
low complexity region 363 373 N/A INTRINSIC
Pfam:Sec16_C 572 769 3.5e-7 PFAM
low complexity region 866 882 N/A INTRINSIC
low complexity region 930 949 N/A INTRINSIC
low complexity region 953 975 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000182812
Predicted Effect probably damaging
Transcript: ENSMUST00000182886
AA Change: T539A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000138213
Gene: ENSMUSG00000035325
AA Change: T539A

DomainStartEndE-ValueType
WD40 56 102 1e-1 SMART
WD40 111 151 3.3e-4 SMART
WD40 158 197 3.2e-3 SMART
WD40 200 245 4.1e-2 SMART
WD40 249 289 1.2e-4 SMART
WD40 292 332 2.6e-5 SMART
low complexity region 363 373 N/A INTRINSIC
Pfam:Sec16_C 532 731 2.1e-6 PFAM
low complexity region 827 843 N/A INTRINSIC
low complexity region 891 910 N/A INTRINSIC
low complexity region 914 936 N/A INTRINSIC
Predicted Effect
Predicted Effect probably damaging
Transcript: ENSMUST00000183247
AA Change: T148A

PolyPhen 2 Score 0.976 (Sensitivity: 0.76; Specificity: 0.96)
SMART Domains Protein: ENSMUSP00000138129
Gene: ENSMUSG00000035325
AA Change: T148A

DomainStartEndE-ValueType
Pfam:Sec16_C 141 248 1.5e-7 PFAM
Meta Mutation Damage Score 0.1734 question?
Coding Region Coverage
  • 1x: 99.9%
  • 3x: 99.5%
  • 10x: 97.5%
  • 20x: 92.0%
Validation Efficiency 96% (54/56)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene shares similarity with the yeast Sec31 protein, and is a component of the outer layer of the coat protein complex II (COPII). The encoded protein is involved in vesicle budding from the endoplasmic reticulum (ER) and contains multiple WD repeats near the N-terminus and a proline-rich region in the C-terminal half. It associates with the protein encoded by the SEC13 homolog, nuclear pore and COPII coat complex component (SEC13), and is required for ER-Golgi transport. Monoubiquitylation of this protein by CUL3-KLHL12 was found to regulate the size of COPII coats to accommodate unusually shaped cargo. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
Allele List at MGI

All alleles(31) : Gene trapped(31)

Other mutations in this stock
Total: 58 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Asb5 T A 8: 55,003,610 (GRCm39) V44E probably damaging Het
Bmpr2 T A 1: 59,907,503 (GRCm39) D865E probably damaging Het
Ccr4 A G 9: 114,322,047 (GRCm39) V6A probably benign Het
Cd209a A T 8: 3,797,031 (GRCm39) D102E probably damaging Het
Cdh18 A G 15: 23,227,022 (GRCm39) D161G possibly damaging Het
Cog4 T A 8: 111,607,526 (GRCm39) I671N possibly damaging Het
Col14a1 T G 15: 55,309,218 (GRCm39) probably benign Het
Cpne6 A G 14: 55,751,110 (GRCm39) D173G probably damaging Het
Daglb G T 5: 143,467,406 (GRCm39) V275L probably benign Het
Defb43 G T 14: 63,249,321 (GRCm39) probably null Het
Dhx30 A G 9: 109,914,120 (GRCm39) V1022A possibly damaging Het
Egfem1 A T 3: 29,711,312 (GRCm39) K297M probably damaging Het
Egfr A G 11: 16,841,259 (GRCm39) I717V probably benign Het
Eif2ak1 T G 5: 143,803,765 (GRCm39) probably null Het
Epb42 T C 2: 120,857,614 (GRCm39) Y307C possibly damaging Het
Erlec1 G A 11: 30,898,442 (GRCm39) Q10* probably null Het
Fam185a A G 5: 21,630,281 (GRCm39) D39G probably benign Het
Fbxl4 T A 4: 22,433,661 (GRCm39) D599E probably damaging Het
Fgfr2 T A 7: 129,802,850 (GRCm39) T268S probably benign Het
Gabra1 A T 11: 42,053,382 (GRCm39) M84K probably benign Het
Gba1 A G 3: 89,113,235 (GRCm39) D222G probably benign Het
Gm3409 T A 5: 146,474,596 (GRCm39) H37Q possibly damaging Het
Gm4559 A G 7: 141,827,887 (GRCm39) C72R unknown Het
Grik4 T C 9: 42,540,304 (GRCm39) N292S probably benign Het
Haao A G 17: 84,139,113 (GRCm39) S274P possibly damaging Het
Hsd17b4 T A 18: 50,305,329 (GRCm39) probably null Het
Igdcc4 A T 9: 65,027,603 (GRCm39) S222C probably damaging Het
Iqub T A 6: 24,449,744 (GRCm39) N707I probably damaging Het
Itgb7 T A 15: 102,124,701 (GRCm39) D772V probably benign Het
Kif14 T C 1: 136,455,149 (GRCm39) L1607P probably damaging Het
Klf5 A G 14: 99,538,817 (GRCm39) T77A probably benign Het
Klhl29 C T 12: 5,141,030 (GRCm39) V605I probably damaging Het
Map4k1 T C 7: 28,686,447 (GRCm39) V105A probably damaging Het
Mctp2 A T 7: 71,850,092 (GRCm39) probably null Het
Med12l A G 3: 59,164,500 (GRCm39) E1364G probably damaging Het
Mup9 A T 4: 60,375,805 (GRCm39) D30E possibly damaging Het
Naip1 T C 13: 100,545,596 (GRCm39) R1311G probably damaging Het
Or2ag2 A G 7: 106,485,604 (GRCm39) V140A probably benign Het
Or2v1 C T 11: 49,025,760 (GRCm39) T247I probably benign Het
Or4f14 G A 2: 111,743,204 (GRCm39) Q24* probably null Het
Or8g28 T A 9: 39,169,378 (GRCm39) M197L probably benign Het
Pkd1l3 A C 8: 110,349,844 (GRCm39) T230P unknown Het
Pthlh G T 6: 147,158,688 (GRCm39) H91N probably damaging Het
Rapgef5 T A 12: 117,681,942 (GRCm39) V239D probably damaging Het
Rita1 G A 5: 120,749,635 (GRCm39) T26I probably damaging Het
Robo3 T C 9: 37,334,586 (GRCm39) T615A probably damaging Het
Rpp38 T C 2: 3,330,644 (GRCm39) D86G probably benign Het
Senp2 G T 16: 21,842,550 (GRCm39) V205L probably damaging Het
Septin10 T C 10: 59,028,133 (GRCm39) N63D possibly damaging Het
Sez6 A G 11: 77,864,670 (GRCm39) Het
Spesp1 C T 9: 62,179,715 (GRCm39) V398I probably benign Het
Tmbim7 G A 5: 3,714,319 (GRCm39) G19S probably benign Het
Tnni3k A T 3: 154,646,695 (GRCm39) L431* probably null Het
Trdn T A 10: 33,340,551 (GRCm39) probably null Het
Tubb2a A G 13: 34,259,442 (GRCm39) V116A possibly damaging Het
Ush1c T C 7: 45,878,643 (GRCm39) D124G probably damaging Het
Zfp768 A T 7: 126,943,827 (GRCm39) F103L probably damaging Het
Zfp799 A G 17: 33,039,820 (GRCm39) S149P probably damaging Het
Other mutations in Sec31a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00657:Sec31a APN 5 100,551,876 (GRCm39) nonsense probably null
IGL01610:Sec31a APN 5 100,550,217 (GRCm39) splice site probably benign
IGL01804:Sec31a APN 5 100,523,065 (GRCm39) critical splice donor site probably null
IGL02026:Sec31a APN 5 100,517,485 (GRCm39) missense probably benign 0.04
IGL02150:Sec31a APN 5 100,533,984 (GRCm39) splice site probably benign
IGL02237:Sec31a APN 5 100,509,914 (GRCm39) missense probably damaging 1.00
IGL02469:Sec31a APN 5 100,533,114 (GRCm39) missense probably benign 0.02
IGL02512:Sec31a APN 5 100,555,052 (GRCm39) missense probably damaging 0.99
control UTSW 5 100,510,032 (GRCm39) missense probably damaging 1.00
D3080:Sec31a UTSW 5 100,511,691 (GRCm39) missense probably damaging 1.00
PIT4142001:Sec31a UTSW 5 100,555,134 (GRCm39) missense probably damaging 1.00
R0366:Sec31a UTSW 5 100,530,625 (GRCm39) missense probably damaging 1.00
R0453:Sec31a UTSW 5 100,551,977 (GRCm39) splice site probably benign
R0511:Sec31a UTSW 5 100,523,099 (GRCm39) missense probably benign 0.01
R0546:Sec31a UTSW 5 100,551,929 (GRCm39) missense probably damaging 1.00
R0675:Sec31a UTSW 5 100,541,066 (GRCm39) missense probably damaging 0.97
R0678:Sec31a UTSW 5 100,555,084 (GRCm39) missense possibly damaging 0.74
R0975:Sec31a UTSW 5 100,543,763 (GRCm39) splice site probably null
R1146:Sec31a UTSW 5 100,510,032 (GRCm39) missense probably damaging 1.00
R1146:Sec31a UTSW 5 100,510,032 (GRCm39) missense probably damaging 1.00
R1540:Sec31a UTSW 5 100,523,178 (GRCm39) missense probably damaging 1.00
R1616:Sec31a UTSW 5 100,534,054 (GRCm39) missense possibly damaging 0.88
R1780:Sec31a UTSW 5 100,529,195 (GRCm39) splice site probably null
R2472:Sec31a UTSW 5 100,533,064 (GRCm39) missense probably damaging 1.00
R3689:Sec31a UTSW 5 100,530,766 (GRCm39) missense probably damaging 1.00
R4515:Sec31a UTSW 5 100,513,817 (GRCm39) missense probably damaging 0.99
R4801:Sec31a UTSW 5 100,541,222 (GRCm39) missense probably damaging 0.96
R4802:Sec31a UTSW 5 100,541,222 (GRCm39) missense probably damaging 0.96
R4896:Sec31a UTSW 5 100,516,192 (GRCm39) missense probably damaging 1.00
R5004:Sec31a UTSW 5 100,516,192 (GRCm39) missense probably damaging 1.00
R5053:Sec31a UTSW 5 100,541,073 (GRCm39) missense possibly damaging 0.94
R5158:Sec31a UTSW 5 100,541,180 (GRCm39) missense probably damaging 0.99
R5191:Sec31a UTSW 5 100,553,370 (GRCm39) missense possibly damaging 0.75
R5222:Sec31a UTSW 5 100,530,754 (GRCm39) missense probably benign
R5405:Sec31a UTSW 5 100,531,657 (GRCm39) nonsense probably null
R5436:Sec31a UTSW 5 100,511,698 (GRCm39) missense probably damaging 0.98
R5577:Sec31a UTSW 5 100,550,133 (GRCm39) missense possibly damaging 0.95
R6005:Sec31a UTSW 5 100,511,737 (GRCm39) missense probably damaging 1.00
R6184:Sec31a UTSW 5 100,517,453 (GRCm39) critical splice donor site probably null
R6245:Sec31a UTSW 5 100,534,043 (GRCm39) missense probably benign 0.07
R6476:Sec31a UTSW 5 100,534,008 (GRCm39) missense probably benign 0.03
R6744:Sec31a UTSW 5 100,540,358 (GRCm39) missense possibly damaging 0.47
R6804:Sec31a UTSW 5 100,530,671 (GRCm39) missense probably benign 0.03
R6911:Sec31a UTSW 5 100,541,123 (GRCm39) missense possibly damaging 0.92
R6936:Sec31a UTSW 5 100,540,369 (GRCm39) missense probably benign
R7345:Sec31a UTSW 5 100,533,129 (GRCm39) missense probably damaging 1.00
R7760:Sec31a UTSW 5 100,540,487 (GRCm39) missense probably damaging 1.00
R7898:Sec31a UTSW 5 100,547,336 (GRCm39) missense probably damaging 0.99
R8088:Sec31a UTSW 5 100,526,721 (GRCm39) missense
R8555:Sec31a UTSW 5 100,540,273 (GRCm39) missense probably benign 0.25
R8762:Sec31a UTSW 5 100,526,688 (GRCm39) missense
R9055:Sec31a UTSW 5 100,534,040 (GRCm39) missense possibly damaging 0.75
R9173:Sec31a UTSW 5 100,529,147 (GRCm39) missense possibly damaging 0.85
R9249:Sec31a UTSW 5 100,533,083 (GRCm39) missense probably damaging 0.98
X0003:Sec31a UTSW 5 100,547,213 (GRCm39) missense probably damaging 0.98
Z1177:Sec31a UTSW 5 100,531,704 (GRCm39) missense probably damaging 1.00
Predicted Primers PCR Primer
(F):5'- ACTCCTATTTCTGTGTCAAACAATT -3'
(R):5'- CAGCTTGTTTAGAAATTTAATCTGCT -3'

Sequencing Primer
(F):5'- CCTCCCGAGTGCTAGGATTAAAG -3'
(R):5'- GTTCTCCACTTGTCTGTGAA -3'
Posted On 2018-05-21