Incidental Mutation 'R9663:Sema5a'
ID 727713
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
Accession Numbers
Essential gene? Essential (E-score: 1.000) question?
Stock # R9663 (G1)
Quality Score 225.009
Status Not validated
Chromosome 15
Chromosomal Location 32244959-32696487 bp(+) (GRCm39)
Type of Mutation nonsense
DNA Base Change (assembly) C to T at 32673546 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Glutamine to Stop codon at position 795 (Q795*)
Ref Sequence ENSEMBL: ENSMUSP00000069024 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000067458]
AlphaFold no structure available at present
Predicted Effect probably null
Transcript: ENSMUST00000067458
AA Change: Q795*
SMART Domains Protein: ENSMUSP00000069024
Gene: ENSMUSG00000022231
AA Change: Q795*

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
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.6%
  • 20x: 98.6%
Validation Efficiency
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: 78 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Alkbh6 T C 7: 30,013,371 (GRCm39) S161P probably damaging Het
Alppl2 T A 1: 87,015,753 (GRCm39) H297L probably benign Het
Angptl2 A G 2: 33,118,231 (GRCm39) R2G probably benign Het
Arhgef15 T A 11: 68,845,255 (GRCm39) N199I probably damaging Het
Asns A T 6: 7,680,132 (GRCm39) I328K probably damaging Het
Atad2 G T 15: 57,971,540 (GRCm39) T734K probably benign Het
Capn3 A C 2: 120,316,859 (GRCm39) M283L probably benign Het
Catsperd T A 17: 56,960,751 (GRCm39) C384S possibly damaging Het
Cd101 A G 3: 100,911,222 (GRCm39) V816A probably benign Het
Cd5 T G 19: 10,703,858 (GRCm39) D68A probably benign Het
Ceacam18 G A 7: 43,288,764 (GRCm39) V172M probably damaging Het
Cfap100 G A 6: 90,386,328 (GRCm39) R276C Het
Clip2 C T 5: 134,533,616 (GRCm39) R487Q probably benign Het
Creb3l2 A G 6: 37,356,926 (GRCm39) V47A probably damaging Het
Crebbp T A 16: 3,933,654 (GRCm39) E1017D probably damaging Het
Cttn T C 7: 144,011,461 (GRCm39) D116G probably damaging Het
Cyp2c65 A G 19: 39,079,070 (GRCm39) probably null Het
Dcaf13 C T 15: 38,982,178 (GRCm39) T48I possibly damaging Het
Dsc2 T A 18: 20,171,205 (GRCm39) D598V probably damaging Het
Dtx3 G A 10: 127,028,518 (GRCm39) T237I probably damaging Het
E130308A19Rik A G 4: 59,719,764 (GRCm39) E432G possibly damaging Het
Eps15 G A 4: 109,179,270 (GRCm39) V219I probably benign Het
Ext1 A G 15: 53,208,456 (GRCm39) S102P probably damaging Het
Fam151a A T 4: 106,604,894 (GRCm39) I419L possibly damaging Het
Fam89a C T 8: 125,478,436 (GRCm39) G38D probably damaging Het
Fdx2 G T 9: 20,984,717 (GRCm39) A29E probably benign Het
Hhla1 G A 15: 65,813,630 (GRCm39) T234I probably damaging Het
Hspb6 G A 7: 30,253,714 (GRCm39) V76M probably damaging Het
Ighmbp2 C A 19: 3,315,325 (GRCm39) K698N probably benign Het
Invs A G 4: 48,426,218 (GRCm39) I1002V probably damaging Het
Itga8 A C 2: 12,196,580 (GRCm39) F612L probably benign Het
Kcnma1 G T 14: 24,053,897 (GRCm39) F99L probably benign Het
Klf11 A G 12: 24,705,731 (GRCm39) Y395C probably damaging Het
Kplce A T 3: 92,776,283 (GRCm39) N133K probably benign Het
Lama4 G A 10: 38,923,944 (GRCm39) E451K probably damaging Het
Lrr1 A G 12: 69,221,884 (GRCm39) Y342C probably damaging Het
Lrrc18 A T 14: 32,731,021 (GRCm39) M187L probably benign Het
Luc7l3 A G 11: 94,187,756 (GRCm39) S311P unknown Het
Lypd3 T A 7: 24,338,349 (GRCm39) S133R probably damaging Het
Mcm5 C T 8: 75,844,168 (GRCm39) S313F probably benign Het
Mug1 T A 6: 121,859,699 (GRCm39) S1233T probably benign Het
Mug1 A T 6: 121,857,463 (GRCm39) E1062D probably benign Het
Myh7 T C 14: 55,221,098 (GRCm39) K942E probably damaging Het
Nedd9 T C 13: 41,469,941 (GRCm39) D404G probably damaging Het
Nisch C A 14: 30,895,625 (GRCm39) A1022S probably damaging Het
Nkx3-1 A G 14: 69,429,321 (GRCm39) D113G probably benign Het
Or1ad6 T C 11: 50,860,165 (GRCm39) F107L probably benign Het
Or6c1b A T 10: 129,272,929 (GRCm39) I83F probably damaging Het
Or6c215 A G 10: 129,637,497 (GRCm39) F299S probably benign Het
Otub1 C T 19: 7,176,813 (GRCm39) G181D probably damaging Het
Palb2 T C 7: 121,726,304 (GRCm39) H522R probably benign Het
Pfpl A T 19: 12,407,459 (GRCm39) D570V probably damaging Het
Phyhd1 A G 2: 30,171,070 (GRCm39) N271S probably damaging Het
Ptprm T C 17: 67,498,291 (GRCm39) Q50R probably benign Het
Rfx2 C A 17: 57,087,895 (GRCm39) V499L possibly damaging Het
Sf3a2 A G 10: 80,637,309 (GRCm39) N49S probably damaging Het
Sft2d1 T G 17: 8,545,812 (GRCm39) S156A probably benign Het
Slc14a1 C A 18: 78,152,807 (GRCm39) A367S probably damaging Het
Slc25a33 T A 4: 149,836,913 (GRCm39) T144S probably benign Het
Slc7a13 A T 4: 19,818,818 (GRCm39) K6M possibly damaging Het
Spata31e5 G T 1: 28,816,536 (GRCm39) H499N probably benign Het
Tfap2c G A 2: 172,399,213 (GRCm39) D487N probably damaging Het
Thbs1 G A 2: 117,949,897 (GRCm39) R624Q probably damaging Het
Thsd4 A G 9: 59,890,026 (GRCm39) F857S probably damaging Het
Tnfrsf4 A G 4: 156,100,884 (GRCm39) I272V probably benign Het
Trak1 C T 9: 121,220,924 (GRCm39) R45C probably benign Het
Trpm2 A G 10: 77,756,320 (GRCm39) S1167P probably benign Het
Ttc14 A T 3: 33,855,537 (GRCm39) T161S probably benign Het
Ttll1 A G 15: 83,380,579 (GRCm39) V262A possibly damaging Het
Ttn C T 2: 76,715,357 (GRCm39) E7912K unknown Het
Ufsp1 C A 5: 137,293,545 (GRCm39) P165Q possibly damaging Het
Usp19 T G 9: 108,371,894 (GRCm39) L390R probably damaging Het
Vegfc G T 8: 54,634,338 (GRCm39) C339F probably damaging Het
Vmn2r6 A T 3: 64,463,549 (GRCm39) N428K possibly damaging Het
Wdr11 T G 7: 129,210,647 (GRCm39) V517G probably damaging Het
Xkr4 T A 1: 3,286,519 (GRCm39) D557V probably benign Het
Zan C A 5: 137,379,119 (GRCm39) C5327F unknown Het
Zfp770 A T 2: 114,026,949 (GRCm39) N373K probably benign 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
R1960:Sema5a UTSW 15 32,562,877 (GRCm39) missense possibly damaging 0.66
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
X0020:Sema5a UTSW 15 32,417,646 (GRCm39) missense probably benign 0.00
Predicted Primers PCR Primer
(F):5'- ACATATTGGAAGCTGCCATTCAG -3'
(R):5'- TCAGTACTTAAAGGCTGCAAGC -3'

Sequencing Primer
(F):5'- TGCCATTCAGCTGCAGTG -3'
(R):5'- GCACACAGCTTTCCCAGTC -3'
Posted On 2022-10-06