Incidental Mutation 'R4980:Sema4d'
ID 384766
Institutional Source Beutler Lab
Gene Symbol Sema4d
Ensembl Gene ENSMUSG00000021451
Gene Name sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4D
Synonyms Semacl2, Semcl2, Semaj, M-sema G, coll-4, CD100, semaphorin H
MMRRC Submission 042575-MU
Accession Numbers
Essential gene? Non essential (E-score: 0.000) question?
Stock # R4980 (G1)
Quality Score 176
Status Not validated
Chromosome 13
Chromosomal Location 51839565-51947783 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 51865270 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Tyrosine to Cysteine at position 358 (Y358C)
Ref Sequence ENSEMBL: ENSMUSP00000105667 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000021900] [ENSMUST00000110039] [ENSMUST00000110040]
AlphaFold O09126
Predicted Effect probably damaging
Transcript: ENSMUST00000021900
AA Change: Y358C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000021900
Gene: ENSMUSG00000021451
AA Change: Y358C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Sema 50 482 7.68e-192 SMART
PSI 502 554 1.41e-12 SMART
IG 561 647 4.78e-1 SMART
transmembrane domain 733 755 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000110039
AA Change: Y358C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105666
Gene: ENSMUSG00000021451
AA Change: Y358C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Sema 50 482 7.68e-192 SMART
PSI 502 554 1.41e-12 SMART
IG 561 647 4.78e-1 SMART
transmembrane domain 733 755 N/A INTRINSIC
Predicted Effect probably damaging
Transcript: ENSMUST00000110040
AA Change: Y358C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
SMART Domains Protein: ENSMUSP00000105667
Gene: ENSMUSG00000021451
AA Change: Y358C

DomainStartEndE-ValueType
signal peptide 1 23 N/A INTRINSIC
Sema 50 482 7.68e-192 SMART
PSI 502 554 1.41e-12 SMART
IG 561 647 4.78e-1 SMART
transmembrane domain 733 755 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000125511
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 96.8%
  • 20x: 93.8%
Validation Efficiency
MGI Phenotype PHENOTYPE: Mice homozygous for disruptions in this gene display functional defects in their immune system but are normal in other systems of the body. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 70 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4930522L14Rik A T 5: 109,885,292 (GRCm39) C189S probably damaging Het
Abcd3 A T 3: 121,562,917 (GRCm39) probably null Het
Adar T C 3: 89,638,121 (GRCm39) S2P probably benign Het
Amhr2 T A 15: 102,362,765 (GRCm39) S511T probably benign Het
Atg16l1 T C 1: 87,694,553 (GRCm39) S77P possibly damaging Het
Bltp1 T C 3: 36,997,461 (GRCm39) S1173P probably damaging Het
Cacna1i T C 15: 80,232,650 (GRCm39) F218L probably damaging Het
Cd5l A T 3: 87,274,908 (GRCm39) H149L probably benign Het
Cdc14a T A 3: 116,186,506 (GRCm39) R92* probably null Het
Col19a1 T C 1: 24,565,564 (GRCm39) T256A unknown Het
Col22a1 C T 15: 71,673,792 (GRCm39) A975T unknown Het
Cracd A T 5: 77,005,421 (GRCm39) D594V unknown Het
Cyp20a1 T C 1: 60,402,373 (GRCm39) W153R probably damaging Het
Dnase1l1 C T X: 73,320,644 (GRCm39) probably null Homo
Dpyd T C 3: 118,710,767 (GRCm39) S392P probably damaging Het
Dst A T 1: 34,295,369 (GRCm39) L957F probably damaging Het
Emilin2 G T 17: 71,560,066 (GRCm39) D970E possibly damaging Het
Fbn2 T C 18: 58,143,703 (GRCm39) E2784G probably benign Het
Fbxw10 T C 11: 62,738,583 (GRCm39) I159T possibly damaging Het
Fgfr2 T C 7: 129,802,810 (GRCm39) Y192C probably damaging Het
Gm7298 A G 6: 121,736,198 (GRCm39) probably null Het
Igf2r C T 17: 12,922,247 (GRCm39) probably null Het
Ints4 T C 7: 97,151,057 (GRCm39) probably null Het
Kcnf1 A G 12: 17,225,012 (GRCm39) F403S possibly damaging Het
Kif11 C T 19: 37,375,819 (GRCm39) Q211* probably null Het
Kif13a A G 13: 46,906,222 (GRCm39) S574P possibly damaging Het
Kifc3 T A 8: 95,853,177 (GRCm39) T60S probably benign Het
Krt82 T C 15: 101,453,534 (GRCm39) D284G possibly damaging Het
Lancl1 T C 1: 67,043,968 (GRCm39) Y344C probably benign Het
Ltbp3 A T 19: 5,803,955 (GRCm39) probably null Het
Map3k4 A G 17: 12,490,958 (GRCm39) F158L probably damaging Het
Mast2 A G 4: 116,174,948 (GRCm39) Y469H probably damaging Het
Mcf2l T G 8: 13,034,883 (GRCm39) F97C probably damaging Het
Mpeg1 T C 19: 12,438,904 (GRCm39) S121P probably damaging Het
Mycbp2 A T 14: 103,497,821 (GRCm39) probably null Het
Myt1l A T 12: 29,877,038 (GRCm39) T230S unknown Het
Naa15 T C 3: 51,366,173 (GRCm39) probably null Het
Nans G A 4: 46,492,764 (GRCm39) R64Q probably benign Het
Nbea C T 3: 55,554,772 (GRCm39) probably null Het
Nbea T C 3: 55,860,466 (GRCm39) E1870G probably benign Het
Ncapd3 T C 9: 26,974,591 (GRCm39) S688P probably damaging Het
Nedd4l G T 18: 65,213,131 (GRCm39) E96* probably null Het
Or56a5 T A 7: 104,793,431 (GRCm39) Y23F probably benign Het
Or5b21 A T 19: 12,839,384 (GRCm39) M82L probably benign Het
Pdxk A G 10: 78,287,318 (GRCm39) L81P probably damaging Het
Plec T A 15: 76,077,495 (GRCm39) R269* probably null Het
Plec T C 15: 76,090,065 (GRCm39) I92V probably damaging Het
Ppara T C 15: 85,671,434 (GRCm39) Y112H probably damaging Het
Ppp2r2c A T 5: 37,109,732 (GRCm39) M364L probably benign Het
Prag1 A C 8: 36,606,740 (GRCm39) H827P probably damaging Het
Ptprg A G 14: 12,154,421 (GRCm38) N714S probably benign Het
Rbp2 G A 9: 98,380,894 (GRCm39) V67I probably benign Het
Rictor T A 15: 6,811,141 (GRCm39) Y835N probably damaging Het
Ripply2 A G 9: 86,901,747 (GRCm39) Q91R probably damaging Het
Sap130 C A 18: 31,782,699 (GRCm39) H203Q possibly damaging Het
Serbp1 G A 6: 67,254,872 (GRCm39) D294N probably benign Het
Slc16a10 A G 10: 39,956,801 (GRCm39) W113R probably damaging Het
Slc6a6 A G 6: 91,703,041 (GRCm39) Y138C probably damaging Het
Spag11a T C 8: 19,207,962 (GRCm39) M1T probably null Het
Spata20 T C 11: 94,375,435 (GRCm39) M120V probably damaging Het
Stk32a A C 18: 43,447,113 (GRCm39) K357Q probably benign Het
Tasor T A 14: 27,183,382 (GRCm39) L614I probably benign Het
Trmo A T 4: 46,389,364 (GRCm39) C10* probably null Het
Tsc22d1 T G 14: 76,655,696 (GRCm39) V643G probably benign Het
Vangl2 A T 1: 171,837,132 (GRCm39) L226I probably damaging Het
Vps35l T A 7: 118,406,232 (GRCm39) D605E probably damaging Het
Wnt3a A T 11: 59,140,626 (GRCm39) C297S probably damaging Het
Wwc1 T C 11: 35,778,930 (GRCm39) K301E possibly damaging Het
Zfhx4 C T 3: 5,464,039 (GRCm39) T1399I possibly damaging Het
Zswim4 C T 8: 84,953,296 (GRCm39) probably null Het
Other mutations in Sema4d
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02131:Sema4d APN 13 51,856,973 (GRCm39) splice site probably null
IGL02155:Sema4d APN 13 51,857,303 (GRCm39) missense probably benign 0.01
IGL02422:Sema4d APN 13 51,857,124 (GRCm39) missense probably benign
IGL02795:Sema4d APN 13 51,857,447 (GRCm39) missense probably benign 0.00
IGL03068:Sema4d APN 13 51,862,922 (GRCm39) missense probably damaging 1.00
IGL03164:Sema4d APN 13 51,862,958 (GRCm39) missense possibly damaging 0.58
R0060:Sema4d UTSW 13 51,859,293 (GRCm39) unclassified probably benign
R0060:Sema4d UTSW 13 51,859,293 (GRCm39) unclassified probably benign
R0305:Sema4d UTSW 13 51,866,764 (GRCm39) missense probably damaging 1.00
R0309:Sema4d UTSW 13 51,879,347 (GRCm39) missense probably benign 0.14
R0708:Sema4d UTSW 13 51,866,755 (GRCm39) missense probably benign 0.17
R1809:Sema4d UTSW 13 51,867,727 (GRCm39) critical splice donor site probably null
R1851:Sema4d UTSW 13 51,865,258 (GRCm39) missense possibly damaging 0.94
R2096:Sema4d UTSW 13 51,864,037 (GRCm39) missense probably damaging 1.00
R2159:Sema4d UTSW 13 51,874,571 (GRCm39) missense probably damaging 1.00
R2367:Sema4d UTSW 13 51,857,176 (GRCm39) intron probably benign
R4329:Sema4d UTSW 13 51,857,340 (GRCm39) missense probably benign
R4372:Sema4d UTSW 13 51,866,767 (GRCm39) missense probably damaging 1.00
R4384:Sema4d UTSW 13 51,856,919 (GRCm39) missense probably damaging 1.00
R4590:Sema4d UTSW 13 51,877,654 (GRCm39) missense probably benign 0.29
R5523:Sema4d UTSW 13 51,865,390 (GRCm39) missense possibly damaging 0.89
R6086:Sema4d UTSW 13 51,867,781 (GRCm39) missense probably damaging 1.00
R7197:Sema4d UTSW 13 51,856,872 (GRCm39) missense probably benign 0.01
R7340:Sema4d UTSW 13 51,877,598 (GRCm39) missense probably damaging 1.00
R7606:Sema4d UTSW 13 51,877,658 (GRCm39) missense probably benign 0.00
R7859:Sema4d UTSW 13 51,876,387 (GRCm39) missense probably benign 0.30
R8193:Sema4d UTSW 13 51,859,192 (GRCm39) nonsense probably null
R8703:Sema4d UTSW 13 51,854,959 (GRCm39) missense
R8796:Sema4d UTSW 13 51,865,546 (GRCm39) missense probably damaging 1.00
R8842:Sema4d UTSW 13 51,863,018 (GRCm39) missense probably benign 0.04
R8904:Sema4d UTSW 13 51,854,935 (GRCm39) nonsense probably null
R9016:Sema4d UTSW 13 51,867,794 (GRCm39) missense probably damaging 1.00
R9115:Sema4d UTSW 13 51,877,596 (GRCm39) missense probably benign
Z1176:Sema4d UTSW 13 51,857,111 (GRCm39) missense probably damaging 0.99
Predicted Primers PCR Primer
(F):5'- GATCAGAAAGGAACAGCTTCAC -3'
(R):5'- AGTTCACTTGTGAGTCCCTTGG -3'

Sequencing Primer
(F):5'- AGCTTCACTGTTCACCCCAGG -3'
(R):5'- AGTTGGGGCCTGGTCAC -3'
Posted On 2016-05-10