Incidental Mutation 'R5208:Sema4c'
ID 402116
Institutional Source Beutler Lab
Gene Symbol Sema4c
Ensembl Gene ENSMUSG00000026121
Gene Name sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C
Synonyms M-Sema F, Semacl1, Semaf, Semai, Semacl1
MMRRC Submission 042783-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R5208 (G1)
Quality Score 225
Status Not validated
Chromosome 1
Chromosomal Location 36587720-36597430 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to A at 36589407 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Aspartic acid to Valine at position 573 (D573V)
Ref Sequence ENSEMBL: ENSMUSP00000141527 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000001172] [ENSMUST00000114991] [ENSMUST00000191642] [ENSMUST00000191677] [ENSMUST00000193382] [ENSMUST00000194894] [ENSMUST00000195620] [ENSMUST00000207843]
AlphaFold Q64151
Predicted Effect probably benign
Transcript: ENSMUST00000001172
SMART Domains Protein: ENSMUSP00000001172
Gene: ENSMUSG00000079610

DomainStartEndE-ValueType
ANK 30 59 8.77e2 SMART
ANK 63 92 1.08e-5 SMART
ANK 96 127 1.27e-2 SMART
ANK 129 158 5.62e-4 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000114991
AA Change: D573V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000110643
Gene: ENSMUSG00000026121
AA Change: D573V

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 53 481 2.54e-183 SMART
PSI 499 552 4.52e-11 SMART
IG 563 647 1.77e-4 SMART
transmembrane domain 665 687 N/A INTRINSIC
low complexity region 754 774 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000191642
AA Change: D573V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000142284
Gene: ENSMUSG00000026121
AA Change: D573V

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 53 481 2.54e-183 SMART
PSI 499 552 4.52e-11 SMART
IG 563 647 1.77e-4 SMART
transmembrane domain 665 687 N/A INTRINSIC
low complexity region 754 774 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000191677
AA Change: D573V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141263
Gene: ENSMUSG00000026121
AA Change: D573V

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 53 481 2.54e-183 SMART
PSI 499 552 4.52e-11 SMART
IG 563 647 1.77e-4 SMART
transmembrane domain 665 687 N/A INTRINSIC
low complexity region 754 774 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000191785
Predicted Effect probably benign
Transcript: ENSMUST00000193382
Predicted Effect probably benign
Transcript: ENSMUST00000194894
SMART Domains Protein: ENSMUSP00000141712
Gene: ENSMUSG00000079610

DomainStartEndE-ValueType
ANK 30 59 5.6e0 SMART
ANK 63 92 7.1e-8 SMART
ANK 96 127 8.2e-5 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000195620
AA Change: D573V

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000141527
Gene: ENSMUSG00000026121
AA Change: D573V

DomainStartEndE-ValueType
signal peptide 1 20 N/A INTRINSIC
Sema 53 481 2.54e-183 SMART
PSI 499 552 4.52e-11 SMART
IG 563 647 1.77e-4 SMART
transmembrane domain 665 687 N/A INTRINSIC
low complexity region 754 774 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000195160
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208690
Predicted Effect probably benign
Transcript: ENSMUST00000207843
Predicted Effect noncoding transcript
Transcript: ENSMUST00000208269
Coding Region Coverage
  • 1x: 99.3%
  • 3x: 98.6%
  • 10x: 97.3%
  • 20x: 95.3%
Validation Efficiency
MGI Phenotype FUNCTION: This gene encodes a member of the semaphorin family of proteins that have diverse functions in neuronal development, heart morphogenesis, vascular growth, tumor progression and immune cell regulation. Lack of the encoded protein in some mice causes exencephaly resulting in neonatal lethality. Mice that bypass exencephaly show no obvious behavioral defects but display distinct pigmentation defects. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2015]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit exencephaly, neonatal lethality, and abnormal cerebellum morphology. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 63 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Aadacl4 A T 4: 144,344,398 (GRCm39) N58I probably benign Het
Adgra3 T C 5: 50,168,857 (GRCm39) D163G probably damaging Het
Alcam C A 16: 52,115,411 (GRCm39) E236* probably null Het
Ank3 G A 10: 69,838,395 (GRCm39) R1566K possibly damaging Het
Aplf G T 6: 87,619,008 (GRCm39) probably null Het
Arl4a A T 12: 40,086,744 (GRCm39) M1K probably null Het
Asic4 A G 1: 75,427,870 (GRCm39) D132G probably damaging Het
Bbs12 T C 3: 37,374,422 (GRCm39) I290T probably benign Het
BC024139 A G 15: 76,008,865 (GRCm39) S290P probably benign Het
Bmp6 G A 13: 38,653,673 (GRCm39) A247T probably benign Het
Cadps A G 14: 12,457,711 (GRCm38) S1057P possibly damaging Het
Caprin1 A C 2: 103,599,778 (GRCm39) probably null Het
Cdc42bpg G A 19: 6,371,750 (GRCm39) R1343K probably benign Het
Cdk18 A T 1: 132,045,218 (GRCm39) probably null Het
Cenpf A T 1: 189,403,243 (GRCm39) probably null Het
Cfhr1 A T 1: 139,484,068 (GRCm39) probably null Het
Chn2 A T 6: 54,272,786 (GRCm39) I201F probably damaging Het
Chrdl2 A G 7: 99,673,129 (GRCm39) D175G probably damaging Het
Disp2 G T 2: 118,622,286 (GRCm39) R1006L probably damaging Het
Dnah2 C T 11: 69,349,746 (GRCm39) R2399Q probably benign Het
Dnah3 C G 7: 119,631,861 (GRCm39) D1365H probably damaging Het
Efcab8 T A 2: 153,644,343 (GRCm39) Y372* probably null Het
Eftud2 G A 11: 102,732,011 (GRCm39) P768S probably damaging Het
Ehmt1 A C 2: 24,691,545 (GRCm39) S1170A probably benign Het
Gdpd4 A C 7: 97,664,118 (GRCm39) K572Q probably benign Het
Gm7356 T C 17: 14,221,456 (GRCm39) E191G probably damaging Het
Gm8674 A T 13: 50,055,957 (GRCm39) noncoding transcript Het
Gulp1 T G 1: 44,820,199 (GRCm39) H235Q probably benign Het
Hormad1 T C 3: 95,485,418 (GRCm39) V202A possibly damaging Het
Inpp5b G A 4: 124,645,110 (GRCm39) D179N possibly damaging Het
Kcnk4 T A 19: 6,905,069 (GRCm39) Y194F possibly damaging Het
Lars1 A C 18: 42,350,622 (GRCm39) S896A probably benign Het
Lonp1 A G 17: 56,924,793 (GRCm39) V538A probably damaging Het
Map3k14 A T 11: 103,129,972 (GRCm39) L315Q probably damaging Het
Met T A 6: 17,526,422 (GRCm39) Y500* probably null Het
Mga T G 2: 119,778,462 (GRCm39) I2093M possibly damaging Het
Mpl T G 4: 118,313,078 (GRCm39) I152L probably benign Het
Mthfsd G A 8: 121,835,058 (GRCm39) probably benign Het
Mup4 A G 4: 59,958,119 (GRCm39) F150L probably damaging Het
Mybph T A 1: 134,121,273 (GRCm39) V11D probably benign Het
Or4f54 A T 2: 111,122,946 (GRCm39) E111V probably damaging Het
Or52n2c A G 7: 104,574,933 (GRCm39) F13L probably benign Het
Or5ak20 T A 2: 85,184,142 (GRCm39) I43F probably benign Het
Pde4a T C 9: 21,114,854 (GRCm39) probably null Het
Pex2 C T 3: 5,626,428 (GRCm39) R127H probably benign Het
Pgap3 A G 11: 98,288,874 (GRCm39) W94R probably damaging Het
Prl4a1 T C 13: 28,202,467 (GRCm39) V14A probably benign Het
Psg25 A T 7: 18,260,460 (GRCm39) I146N probably benign Het
Ptprn2 A G 12: 116,822,548 (GRCm39) Y209C probably damaging Het
Scart2 C A 7: 139,877,949 (GRCm39) A977D probably benign Het
Setx A T 2: 29,056,379 (GRCm39) I2192F possibly damaging Het
Skic3 G A 13: 76,295,886 (GRCm39) E1050K possibly damaging Het
Sp4 A G 12: 118,263,281 (GRCm39) L255P probably damaging Het
Spaca7 A G 8: 12,636,456 (GRCm39) Y94C probably damaging Het
Stt3a T G 9: 36,657,891 (GRCm39) I390L possibly damaging Het
Tars2 A G 3: 95,654,905 (GRCm39) W128R probably damaging Het
Tll1 G A 8: 64,504,527 (GRCm39) T623M probably damaging Het
Tmem129 A T 5: 33,812,850 (GRCm39) V166E probably damaging Het
Tmem200a T A 10: 25,870,051 (GRCm39) I73F probably benign Het
Tnks1bp1 T C 2: 84,900,976 (GRCm39) M1561T probably damaging Het
Zfat A T 15: 68,052,570 (GRCm39) I401N probably damaging Het
Zfp142 A T 1: 74,610,027 (GRCm39) V1153E probably benign Het
Zwilch T C 9: 64,060,205 (GRCm39) I354V probably benign Het
Other mutations in Sema4c
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00420:Sema4c APN 1 36,593,001 (GRCm39) critical splice donor site probably benign 0.00
IGL01824:Sema4c APN 1 36,592,110 (GRCm39) missense possibly damaging 0.76
IGL02236:Sema4c APN 1 36,592,166 (GRCm39) missense probably damaging 1.00
IGL02262:Sema4c APN 1 36,589,422 (GRCm39) missense probably damaging 1.00
IGL02282:Sema4c APN 1 36,589,284 (GRCm39) splice site probably null
IGL02476:Sema4c APN 1 36,595,031 (GRCm39) missense probably damaging 0.98
IGL02900:Sema4c APN 1 36,589,826 (GRCm39) nonsense probably null
swirl UTSW 1 36,589,392 (GRCm39) missense probably damaging 1.00
IGL02837:Sema4c UTSW 1 36,591,965 (GRCm39) missense probably damaging 1.00
R0427:Sema4c UTSW 1 36,592,892 (GRCm39) nonsense probably null
R0497:Sema4c UTSW 1 36,588,689 (GRCm39) missense probably benign 0.04
R1066:Sema4c UTSW 1 36,589,281 (GRCm39) missense possibly damaging 0.95
R1099:Sema4c UTSW 1 36,591,191 (GRCm39) missense probably damaging 1.00
R1146:Sema4c UTSW 1 36,589,646 (GRCm39) missense probably benign 0.04
R1146:Sema4c UTSW 1 36,589,646 (GRCm39) missense probably benign 0.04
R1639:Sema4c UTSW 1 36,592,615 (GRCm39) missense probably benign 0.00
R1644:Sema4c UTSW 1 36,589,885 (GRCm39) missense probably damaging 1.00
R3176:Sema4c UTSW 1 36,588,960 (GRCm39) missense possibly damaging 0.65
R3177:Sema4c UTSW 1 36,588,960 (GRCm39) missense possibly damaging 0.65
R3276:Sema4c UTSW 1 36,588,960 (GRCm39) missense possibly damaging 0.65
R3277:Sema4c UTSW 1 36,588,960 (GRCm39) missense possibly damaging 0.65
R3551:Sema4c UTSW 1 36,592,804 (GRCm39) missense probably benign 0.02
R4452:Sema4c UTSW 1 36,592,837 (GRCm39) missense probably benign 0.31
R4883:Sema4c UTSW 1 36,591,097 (GRCm39) missense probably damaging 0.98
R4895:Sema4c UTSW 1 36,592,651 (GRCm39) splice site probably null
R4913:Sema4c UTSW 1 36,589,266 (GRCm39) missense probably benign 0.11
R4944:Sema4c UTSW 1 36,589,392 (GRCm39) missense probably damaging 1.00
R5062:Sema4c UTSW 1 36,592,059 (GRCm39) critical splice donor site probably null
R5077:Sema4c UTSW 1 36,590,812 (GRCm39) missense probably benign 0.20
R5109:Sema4c UTSW 1 36,591,381 (GRCm39) frame shift probably null
R5551:Sema4c UTSW 1 36,591,398 (GRCm39) missense probably damaging 1.00
R5912:Sema4c UTSW 1 36,593,469 (GRCm39) missense possibly damaging 0.83
R6578:Sema4c UTSW 1 36,589,834 (GRCm39) missense probably benign 0.02
R7111:Sema4c UTSW 1 36,592,160 (GRCm39) missense possibly damaging 0.48
R7141:Sema4c UTSW 1 36,592,101 (GRCm39) missense probably damaging 0.99
R7252:Sema4c UTSW 1 36,589,096 (GRCm39) missense probably damaging 1.00
R7495:Sema4c UTSW 1 36,589,774 (GRCm39) missense probably benign 0.00
R7891:Sema4c UTSW 1 36,588,995 (GRCm39) missense probably damaging 0.98
R7895:Sema4c UTSW 1 36,592,199 (GRCm39) missense probably damaging 1.00
R8264:Sema4c UTSW 1 36,591,966 (GRCm39) missense probably damaging 1.00
R8478:Sema4c UTSW 1 36,590,871 (GRCm39) missense probably benign 0.04
R8680:Sema4c UTSW 1 36,589,867 (GRCm39) missense probably benign 0.00
R8733:Sema4c UTSW 1 36,591,954 (GRCm39) missense probably damaging 1.00
R9017:Sema4c UTSW 1 36,592,079 (GRCm39) missense probably damaging 1.00
R9344:Sema4c UTSW 1 36,592,395 (GRCm39) missense probably damaging 1.00
R9488:Sema4c UTSW 1 36,591,067 (GRCm39) missense probably benign
X0019:Sema4c UTSW 1 36,592,077 (GRCm39) missense probably damaging 1.00
X0028:Sema4c UTSW 1 36,589,047 (GRCm39) missense possibly damaging 0.95
Predicted Primers PCR Primer
(F):5'- TCTGAATAGCAACGATAGGGTCC -3'
(R):5'- CATGTGGCGAACTTGGACAC -3'

Sequencing Primer
(F):5'- TCCAGAGTGACGGGACTGTG -3'
(R):5'- CGAACTTGGACACTTCAAAGATGTG -3'
Posted On 2016-07-22