Incidental Mutation 'R1960:Sema5a'
ID 318072
Institutional Source Beutler Lab
Gene Symbol Sema5a
Ensembl Gene ENSMUSG00000022231
Gene Name sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A
Synonyms M-Sema D, semF, Semaf, 9130201M22Rik
MMRRC Submission 039974-MU
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R1960 (G1)
Quality Score 225
Status Validated
Chromosome 15
Chromosomal Location 32244959-32696487 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 32562877 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Phenylalanine to Serine at position 296 (F296S)
Ref Sequence ENSEMBL: ENSMUSP00000069024 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000067458]
AlphaFold no structure available at present
Predicted Effect possibly damaging
Transcript: ENSMUST00000067458
AA Change: F296S

PolyPhen 2 Score 0.661 (Sensitivity: 0.86; Specificity: 0.91)
SMART Domains Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: F296S

DomainStartEndE-ValueType
signal peptide 1 22 N/A INTRINSIC
Sema 58 468 2.18e-173 SMART
PSI 486 533 1.78e-9 SMART
TSP1 543 597 2.23e-1 SMART
TSP1 598 651 2.05e-15 SMART
TSP1 656 702 6.94e-13 SMART
low complexity region 707 715 N/A INTRINSIC
low complexity region 755 771 N/A INTRINSIC
TSP1 787 839 4.17e-16 SMART
TSP1 844 896 9.08e-17 SMART
TSP1 899 946 3.19e-3 SMART
low complexity region 949 960 N/A INTRINSIC
transmembrane domain 971 993 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000226876
Predicted Effect noncoding transcript
Transcript: ENSMUST00000227802
Predicted Effect noncoding transcript
Transcript: ENSMUST00000227976
Predicted Effect noncoding transcript
Transcript: ENSMUST00000228015
Predicted Effect noncoding transcript
Transcript: ENSMUST00000228442
Predicted Effect noncoding transcript
Transcript: ENSMUST00000228555
Meta Mutation Damage Score 0.1281 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.6%
  • 10x: 97.1%
  • 20x: 94.9%
Validation Efficiency 100% (95/95)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the semaphorin gene family that encodes membrane proteins containing a semaphorin domain and several thrombospondin type-1 repeats. Members of this family are involved in axonal guidance during neural development. This gene has been implicated as an autism susceptibility gene.[provided by RefSeq, Jan 2010]
PHENOTYPE: Mice homozygous for one null mutation die during organogenesis and display defects in branching of cranial vessels. Mice homozygous for another null mutation appear normal. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 92 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
2410004B18Rik C T 3: 145,643,976 (GRCm39) P55S probably damaging Het
Adgre4 T C 17: 56,098,497 (GRCm39) S136P probably benign Het
Aoc1l1 C T 6: 48,952,687 (GRCm39) T204I probably damaging Het
Arap1 C A 7: 101,022,222 (GRCm39) A8E probably damaging Het
Arid1a A T 4: 133,480,401 (GRCm39) H174Q possibly damaging Het
Btbd2 A G 10: 80,480,539 (GRCm39) I358T probably benign Het
Camkk2 G A 5: 122,875,575 (GRCm39) R492* probably null Het
Capn3 T C 2: 120,294,421 (GRCm39) V23A probably benign Het
Carm1 T G 9: 21,491,606 (GRCm39) V225G probably benign Het
Ccdc113 T A 8: 96,267,459 (GRCm39) N141K probably benign Het
Ccdc60 C A 5: 116,284,243 (GRCm39) M298I probably benign Het
Celsr3 C T 9: 108,723,016 (GRCm39) P2801L probably benign Het
Clec4n T A 6: 123,207,505 (GRCm39) V23E probably damaging Het
Cmtr2 T G 8: 110,948,382 (GRCm39) L231V probably damaging Het
Csrnp3 T G 2: 65,853,363 (GRCm39) V585G probably null Het
Ctnnd2 T C 15: 30,647,257 (GRCm39) S318P probably damaging Het
Cubn A T 2: 13,344,828 (GRCm39) probably null Het
Dgkd C A 1: 87,857,549 (GRCm39) P754T possibly damaging Het
Dnah7a A G 1: 53,724,142 (GRCm39) S108P probably benign Het
Dnajc24 A G 2: 105,832,268 (GRCm39) probably benign Het
Dner A T 1: 84,423,177 (GRCm39) S475R probably damaging Het
Dtnb T C 12: 3,831,190 (GRCm39) L630P probably benign Het
Dysf T C 6: 84,050,885 (GRCm39) F411L probably benign Het
Fbh1 G A 2: 11,762,339 (GRCm39) A566V probably damaging Het
Fbxw19 G T 9: 109,315,004 (GRCm39) T186K probably benign Het
Flacc1 A T 1: 58,698,437 (GRCm39) V327D possibly damaging Het
Gm4825 A G 15: 85,395,245 (GRCm39) noncoding transcript Het
Grhl2 T A 15: 37,336,558 (GRCm39) V54D probably damaging Het
Hmcn1 T C 1: 150,551,742 (GRCm39) I2621V probably benign Het
Hmcn1 T A 1: 150,553,127 (GRCm39) E2521V possibly damaging Het
Kcng1 A G 2: 168,104,904 (GRCm39) V314A probably benign Het
Kif13a G A 13: 47,018,314 (GRCm39) probably benign Het
Kif21a G A 15: 90,855,051 (GRCm39) A703V probably damaging Het
Kifc1 A G 17: 34,103,561 (GRCm39) probably null Het
Klk13 T A 7: 43,370,431 (GRCm39) N31K possibly damaging Het
Klri1 T A 6: 129,674,347 (GRCm39) H221L probably benign Het
Ltbp4 G A 7: 27,028,443 (GRCm39) P273L unknown Het
Med16 T C 10: 79,742,929 (GRCm39) H14R possibly damaging Het
Mpeg1 G A 19: 12,440,275 (GRCm39) V578M probably damaging Het
Mrgpra2a T A 7: 47,076,983 (GRCm39) I92F probably benign Het
Muc5b T C 7: 141,416,374 (GRCm39) C3107R possibly damaging Het
Myo5a T A 9: 75,055,139 (GRCm39) F441I probably damaging Het
Ndst4 T A 3: 125,232,331 (GRCm39) L300* probably null Het
Nlgn2 G T 11: 69,718,136 (GRCm39) D356E probably damaging Het
Nlrp2 T C 7: 5,330,737 (GRCm39) E553G probably damaging Het
Oas1f G A 5: 120,994,502 (GRCm39) C341Y possibly damaging Het
Olfm5 A T 7: 103,809,619 (GRCm39) C111S possibly damaging Het
Oplah G A 15: 76,181,664 (GRCm39) T1119I probably damaging Het
Or2ag15 T C 7: 106,340,601 (GRCm39) E180G probably damaging Het
Or5d46 T C 2: 88,170,545 (GRCm39) L212P probably damaging Het
Or6c74 C T 10: 129,870,187 (GRCm39) Q231* probably null Het
Or6f2 A T 7: 139,756,596 (GRCm39) I188L probably benign Het
Or8b12c A G 9: 37,715,242 (GRCm39) I12V probably benign Het
Or8g51 T A 9: 38,609,500 (GRCm39) H58L probably benign Het
Pde10a T C 17: 9,161,750 (GRCm39) I477T possibly damaging Het
Pde4b A G 4: 102,454,657 (GRCm39) E108G probably damaging Het
Pdgfrb A T 18: 61,198,855 (GRCm39) T338S probably benign Het
Pgghg A G 7: 140,523,260 (GRCm39) M180V probably benign Het
Phactr4 G A 4: 132,104,559 (GRCm39) T256I probably benign Het
Pot1b A T 17: 55,969,531 (GRCm39) Y546N probably damaging Het
Rangap1 T C 15: 81,590,704 (GRCm39) T463A probably benign Het
Rap1gds1 T C 3: 138,756,317 (GRCm39) I13V probably null Het
Rbak A T 5: 143,160,437 (GRCm39) Y205* probably null Het
Reg3b A T 6: 78,348,797 (GRCm39) K31M probably damaging Het
Rfpl4 A T 7: 5,118,533 (GRCm39) Y12* probably null Het
Rnase6 A G 14: 51,367,889 (GRCm39) N94D possibly damaging Het
Rtn4 T C 11: 29,686,464 (GRCm39) L273P probably damaging Het
Ryr3 A C 2: 112,624,812 (GRCm39) F2203V probably damaging Het
Sae1 A T 7: 16,102,490 (GRCm39) D161E possibly damaging Het
Sh3rf1 C A 8: 61,837,897 (GRCm39) P814Q probably damaging Het
Slc22a29 C A 19: 8,146,557 (GRCm39) R415M probably benign Het
Slc25a25 C T 2: 32,310,663 (GRCm39) probably null Het
Slco4c1 T A 1: 96,795,654 (GRCm39) M135L probably benign Het
Slfn1 A G 11: 83,012,579 (GRCm39) I232V possibly damaging Het
Slitrk1 T A 14: 109,149,622 (GRCm39) N363I probably damaging Het
Srr A G 11: 74,799,542 (GRCm39) V311A probably damaging Het
Tasor T C 14: 27,160,621 (GRCm39) S128P probably damaging Het
Tasor C T 14: 27,201,746 (GRCm39) H1419Y possibly damaging Het
Tenm1 T C X: 41,916,078 (GRCm39) D402G probably benign Het
Topors T C 4: 40,261,044 (GRCm39) R747G unknown Het
Trank1 A T 9: 111,220,696 (GRCm39) I2478F probably damaging Het
Trim69 A G 2: 121,998,165 (GRCm39) N46D probably benign Het
Trpm1 T A 7: 63,879,978 (GRCm39) L661Q probably damaging Het
Ttbk1 A C 17: 46,791,150 (GRCm39) F45V probably damaging Het
Ttn T C 2: 76,644,649 (GRCm39) K4708R probably damaging Het
Unkl A G 17: 25,428,619 (GRCm39) probably benign Het
Uros A T 7: 133,288,735 (GRCm39) N257K probably benign Het
Usp25 A G 16: 76,873,259 (GRCm39) Y439C probably damaging Het
Vgf A G 5: 137,061,029 (GRCm39) probably benign Het
Vmn2r8 A T 5: 108,947,152 (GRCm39) D533E probably damaging Het
Vps13a A T 19: 16,702,995 (GRCm39) Y653N probably damaging Het
Zfp358 T C 8: 3,545,742 (GRCm39) V135A possibly damaging Het
Other mutations in Sema5a
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00672:Sema5a APN 15 32,619,026 (GRCm39) missense probably benign 0.06
IGL01148:Sema5a APN 15 32,681,641 (GRCm39) missense probably benign 0.00
IGL01285:Sema5a APN 15 32,575,143 (GRCm39) missense possibly damaging 0.66
IGL01647:Sema5a APN 15 32,417,587 (GRCm39) missense possibly damaging 0.82
IGL01845:Sema5a APN 15 32,474,514 (GRCm39) splice site probably benign
IGL01970:Sema5a APN 15 32,686,792 (GRCm39) missense probably benign 0.02
IGL01986:Sema5a APN 15 32,682,506 (GRCm39) splice site probably benign
IGL02053:Sema5a APN 15 32,550,413 (GRCm39) missense probably benign 0.00
IGL02234:Sema5a APN 15 32,679,318 (GRCm39) missense probably damaging 1.00
IGL02325:Sema5a APN 15 32,686,977 (GRCm39) missense possibly damaging 0.63
IGL02370:Sema5a APN 15 32,682,445 (GRCm39) splice site probably benign
IGL02427:Sema5a APN 15 32,673,690 (GRCm39) splice site probably benign
IGL02621:Sema5a APN 15 32,538,802 (GRCm39) splice site probably benign
IGL02656:Sema5a APN 15 32,631,431 (GRCm39) missense possibly damaging 0.95
IGL03091:Sema5a APN 15 32,538,880 (GRCm39) splice site probably benign
IGL03107:Sema5a APN 15 32,669,554 (GRCm39) missense probably damaging 0.98
IGL03114:Sema5a APN 15 32,673,573 (GRCm39) missense probably damaging 0.99
IGL03222:Sema5a APN 15 32,628,304 (GRCm39) missense probably benign 0.32
PIT4305001:Sema5a UTSW 15 32,628,345 (GRCm39) missense probably benign
R0190:Sema5a UTSW 15 32,562,920 (GRCm39) missense possibly damaging 0.93
R0409:Sema5a UTSW 15 32,681,755 (GRCm39) missense probably damaging 1.00
R0413:Sema5a UTSW 15 32,669,590 (GRCm39) missense probably damaging 1.00
R0504:Sema5a UTSW 15 32,574,949 (GRCm39) splice site probably benign
R1235:Sema5a UTSW 15 32,609,372 (GRCm39) missense probably benign 0.04
R1484:Sema5a UTSW 15 32,460,431 (GRCm39) missense probably damaging 1.00
R1550:Sema5a UTSW 15 32,618,995 (GRCm39) missense probably benign 0.00
R1557:Sema5a UTSW 15 32,460,418 (GRCm39) missense probably benign 0.04
R1670:Sema5a UTSW 15 32,548,945 (GRCm39) missense probably damaging 1.00
R1688:Sema5a UTSW 15 32,669,570 (GRCm39) missense probably benign 0.01
R1760:Sema5a UTSW 15 32,641,252 (GRCm39) missense probably damaging 0.99
R1967:Sema5a UTSW 15 32,681,765 (GRCm39) missense probably damaging 0.99
R2062:Sema5a UTSW 15 32,609,363 (GRCm39) splice site probably benign
R2082:Sema5a UTSW 15 32,619,002 (GRCm39) missense probably benign 0.04
R2218:Sema5a UTSW 15 32,631,455 (GRCm39) missense probably damaging 0.99
R2267:Sema5a UTSW 15 32,575,065 (GRCm39) missense probably benign 0.03
R2299:Sema5a UTSW 15 32,562,922 (GRCm39) missense possibly damaging 0.95
R2438:Sema5a UTSW 15 32,550,399 (GRCm39) missense possibly damaging 0.63
R2698:Sema5a UTSW 15 32,673,546 (GRCm39) missense probably damaging 1.00
R3950:Sema5a UTSW 15 32,689,484 (GRCm39) missense probably damaging 1.00
R4197:Sema5a UTSW 15 32,619,064 (GRCm39) missense probably benign
R4496:Sema5a UTSW 15 32,641,133 (GRCm39) missense probably damaging 1.00
R4840:Sema5a UTSW 15 32,550,400 (GRCm39) missense possibly damaging 0.63
R4842:Sema5a UTSW 15 32,609,563 (GRCm39) missense probably benign
R4867:Sema5a UTSW 15 32,550,436 (GRCm39) missense possibly damaging 0.60
R4934:Sema5a UTSW 15 32,679,310 (GRCm39) missense probably damaging 1.00
R4977:Sema5a UTSW 15 32,679,332 (GRCm39) missense probably damaging 1.00
R5204:Sema5a UTSW 15 32,686,793 (GRCm39) missense probably benign 0.00
R5580:Sema5a UTSW 15 32,575,031 (GRCm39) missense probably benign 0.00
R5937:Sema5a UTSW 15 32,574,987 (GRCm39) missense probably damaging 1.00
R6220:Sema5a UTSW 15 32,686,875 (GRCm39) missense probably damaging 0.99
R6897:Sema5a UTSW 15 32,550,421 (GRCm39) missense probably benign 0.05
R7037:Sema5a UTSW 15 32,686,993 (GRCm39) missense probably damaging 1.00
R7072:Sema5a UTSW 15 32,575,105 (GRCm39) missense possibly damaging 0.94
R7273:Sema5a UTSW 15 32,417,608 (GRCm39) missense probably benign
R7572:Sema5a UTSW 15 32,673,574 (GRCm39) missense probably damaging 1.00
R7621:Sema5a UTSW 15 32,609,378 (GRCm39) missense possibly damaging 0.65
R7642:Sema5a UTSW 15 32,682,471 (GRCm39) missense probably damaging 0.97
R7870:Sema5a UTSW 15 32,609,485 (GRCm39) missense probably benign 0.23
R7880:Sema5a UTSW 15 32,686,954 (GRCm39) missense probably damaging 1.00
R8025:Sema5a UTSW 15 32,548,928 (GRCm39) missense probably benign 0.37
R8034:Sema5a UTSW 15 32,574,987 (GRCm39) missense probably damaging 1.00
R8241:Sema5a UTSW 15 32,575,064 (GRCm39) missense probably benign
R8539:Sema5a UTSW 15 32,618,989 (GRCm39) missense probably damaging 0.98
R8728:Sema5a UTSW 15 32,562,703 (GRCm39) missense probably damaging 0.98
R8807:Sema5a UTSW 15 32,562,868 (GRCm39) missense possibly damaging 0.83
R8825:Sema5a UTSW 15 32,689,498 (GRCm39) missense probably benign 0.02
R9109:Sema5a UTSW 15 32,619,040 (GRCm39) missense probably benign 0.02
R9235:Sema5a UTSW 15 32,619,034 (GRCm39) missense probably benign 0.01
R9298:Sema5a UTSW 15 32,619,040 (GRCm39) missense probably benign 0.02
R9354:Sema5a UTSW 15 32,562,902 (GRCm39) nonsense probably null
R9515:Sema5a UTSW 15 32,679,373 (GRCm39) missense probably damaging 1.00
R9663:Sema5a UTSW 15 32,673,546 (GRCm39) nonsense probably null
X0020:Sema5a UTSW 15 32,417,646 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- TGTGTCTTCCTACGACATCGG -3'
(R):5'- CTGTTGGCCCAGGAAAATAAG -3'

Sequencing Primer
(F):5'- TTCTTCCGAGAAAACGCCGTG -3'
(R):5'- TAAGAAAGACTTCCTCTAGAGCAAC -3'
Posted On 2015-05-19