Incidental Mutation 'R1609:Tspan4'
ID 176674
Institutional Source Beutler Lab
Gene Symbol Tspan4
Ensembl Gene ENSMUSG00000025511
Gene Name tetraspanin 4
Synonyms D130042I01Rik, Tm4sf7, Tspan-4, NAG-2, novel antigen 2
MMRRC Submission 039646-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.073) question?
Stock # R1609 (G1)
Quality Score 225
Status Validated
Chromosome 7
Chromosomal Location 141055194-141073340 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) A to G at 141071557 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 135 (T135A)
Ref Sequence ENSEMBL: ENSMUSP00000113085 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000026585] [ENSMUST00000026586] [ENSMUST00000117634] [ENSMUST00000118694] [ENSMUST00000138092] [ENSMUST00000146305] [ENSMUST00000209452] [ENSMUST00000166082] [ENSMUST00000140858] [ENSMUST00000153191]
AlphaFold Q9DCK3
Predicted Effect probably damaging
Transcript: ENSMUST00000026585
AA Change: T135A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000026585
Gene: ENSMUSG00000025511
AA Change: T135A

DomainStartEndE-ValueType
Pfam:Tetraspannin 8 230 4.7e-55 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000026586
SMART Domains Protein: ENSMUSP00000026586
Gene: ENSMUSG00000025512

DomainStartEndE-ValueType
PDB:3BXW|A 4 240 1e-142 PDB
Blast:Glyco_18 82 302 1e-139 BLAST
SCOP:d1e9la1 84 240 1e-15 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000064642
SMART Domains Protein: ENSMUSP00000065953
Gene: ENSMUSG00000025512

DomainStartEndE-ValueType
PDB:3BXW|A 3 236 1e-143 PDB
Blast:Glyco_18 81 268 1e-121 BLAST
SCOP:d1e9la1 83 236 2e-16 SMART
Predicted Effect probably damaging
Transcript: ENSMUST00000117634
AA Change: T135A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)
SMART Domains Protein: ENSMUSP00000113085
Gene: ENSMUSG00000025511
AA Change: T135A

DomainStartEndE-ValueType
Pfam:Tetraspannin 8 230 1.1e-53 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118694
SMART Domains Protein: ENSMUSP00000112891
Gene: ENSMUSG00000025512

DomainStartEndE-ValueType
PDB:3BXW|A 1 237 1e-142 PDB
Blast:Glyco_18 79 299 1e-139 BLAST
SCOP:d1e9la1 81 237 1e-15 SMART
Predicted Effect noncoding transcript
Transcript: ENSMUST00000130402
Predicted Effect possibly damaging
Transcript: ENSMUST00000138092
AA Change: T135A

PolyPhen 2 Score 0.834 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000115421
Gene: ENSMUSG00000025511
AA Change: T135A

DomainStartEndE-ValueType
Pfam:Tetraspannin 8 154 1.8e-38 PFAM
Predicted Effect possibly damaging
Transcript: ENSMUST00000146305
AA Change: T135A

PolyPhen 2 Score 0.834 (Sensitivity: 0.84; Specificity: 0.93)
SMART Domains Protein: ENSMUSP00000118533
Gene: ENSMUSG00000025511
AA Change: T135A

DomainStartEndE-ValueType
Pfam:Tetraspannin 8 158 2.5e-41 PFAM
Predicted Effect noncoding transcript
Transcript: ENSMUST00000147610
Predicted Effect probably benign
Transcript: ENSMUST00000209452
Predicted Effect probably benign
Transcript: ENSMUST00000166082
SMART Domains Protein: ENSMUSP00000130360
Gene: ENSMUSG00000025512

DomainStartEndE-ValueType
low complexity region 25 35 N/A INTRINSIC
Glyco_18 82 388 3.54e-27 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000140858
Predicted Effect probably benign
Transcript: ENSMUST00000153191
SMART Domains Protein: ENSMUSP00000114693
Gene: ENSMUSG00000025512

DomainStartEndE-ValueType
low complexity region 22 32 N/A INTRINSIC
Glyco_18 79 385 3.54e-27 SMART
Meta Mutation Damage Score 0.4338 question?
Coding Region Coverage
  • 1x: 98.9%
  • 3x: 98.0%
  • 10x: 95.1%
  • 20x: 88.1%
Validation Efficiency 96% (49/51)
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene is a member of the transmembrane 4 superfamily, also known as the tetraspanin family. Most of these members are cell-surface proteins that are characterized by the presence of four hydrophobic domains. The proteins mediate signal transduction events that play a role in the regulation of cell development, activation, growth and motility. This encoded protein is a cell surface glycoprotein and is similar in sequence to its family member CD53 antigen. It is known to complex with integrins and other transmembrane 4 superfamily proteins. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Allele List at MGI
Other mutations in this stock
Total: 38 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Acot2 C T 12: 84,039,630 (GRCm39) R380C possibly damaging Het
Allc A T 12: 28,603,993 (GRCm39) D363E probably damaging Het
Anxa2 TCCC TCC 9: 69,397,036 (GRCm39) probably null Het
App C A 16: 84,876,837 (GRCm39) V185L probably damaging Het
Atp5if1 T C 4: 132,258,078 (GRCm39) D47G probably benign Het
Auh G A 13: 52,989,532 (GRCm39) P308L probably benign Het
Cbr4 T A 8: 61,956,192 (GRCm39) Y220N probably damaging Het
Ccdc6 C A 10: 70,002,877 (GRCm39) Q203K probably damaging Het
Cntnap2 T C 6: 45,992,264 (GRCm39) V397A probably benign Het
Dmxl2 A G 9: 54,316,547 (GRCm39) I1613T possibly damaging Het
Dnah14 T C 1: 181,577,742 (GRCm39) S3020P probably damaging Het
Dnah7b T C 1: 46,392,126 (GRCm39) L3829P probably damaging Het
Fbxw25 C T 9: 109,492,578 (GRCm39) C53Y probably benign Het
Fndc1 G T 17: 7,991,598 (GRCm39) H699Q unknown Het
Gnaq G A 19: 16,360,618 (GRCm39) V314M possibly damaging Het
Gpr158 A G 2: 21,788,104 (GRCm39) T582A possibly damaging Het
Mapk1 T C 16: 16,856,170 (GRCm39) probably benign Het
Med1 T A 11: 98,051,996 (GRCm39) H456L possibly damaging Het
Myo6 G A 9: 80,195,499 (GRCm39) probably null Het
Nipbl A G 15: 8,396,148 (GRCm39) Y142H probably damaging Het
Or4c113 A T 2: 88,885,688 (GRCm39) F27L probably benign Het
Or8k24 A G 2: 86,215,838 (GRCm39) I308T probably benign Het
Or8k33 A C 2: 86,383,949 (GRCm39) V173G probably damaging Het
Pgbd5 T C 8: 125,160,750 (GRCm39) D39G probably benign Het
Pnisr G T 4: 21,871,440 (GRCm39) G387* probably null Het
Pnpla6 T C 8: 3,567,135 (GRCm39) L61P probably damaging Het
Prkra A T 2: 76,463,936 (GRCm39) I242N probably benign Het
Rp1 A G 1: 4,419,424 (GRCm39) S563P probably damaging Het
Rtp3 A G 9: 110,815,085 (GRCm39) probably benign Het
Sema3d A G 5: 12,591,023 (GRCm39) T301A probably damaging Het
Setmar A G 6: 108,053,076 (GRCm39) D190G probably benign Het
Sf3b2 A G 19: 5,345,061 (GRCm39) probably benign Het
Taf4b A G 18: 14,968,938 (GRCm39) K692E probably damaging Het
Tktl2 A G 8: 66,965,504 (GRCm39) E354G probably benign Het
Vmn1r22 G T 6: 57,877,733 (GRCm39) Y81* probably null Het
Vmn2r31 T C 7: 7,387,888 (GRCm39) E561G probably damaging Het
Xrn1 A T 9: 95,856,946 (GRCm39) K389N probably benign Het
Zfp277 A T 12: 40,378,719 (GRCm39) N379K probably damaging Het
Other mutations in Tspan4
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02701:Tspan4 APN 7 141,071,941 (GRCm39) missense probably damaging 0.98
IGL03220:Tspan4 APN 7 141,071,712 (GRCm39) missense probably damaging 1.00
R5286:Tspan4 UTSW 7 141,062,483 (GRCm39) splice site probably null
R5335:Tspan4 UTSW 7 141,069,528 (GRCm39) missense probably damaging 1.00
R8343:Tspan4 UTSW 7 141,071,718 (GRCm39) missense probably damaging 1.00
R9027:Tspan4 UTSW 7 141,069,577 (GRCm39) missense probably benign
R9098:Tspan4 UTSW 7 141,071,816 (GRCm39) missense probably benign 0.18
Predicted Primers PCR Primer
(F):5'- TCTCAGGAAACAAGCAAGAGGTTCG -3'
(R):5'- GTACCAGGTTCATGTAACCCACAGC -3'

Sequencing Primer
(F):5'- CAAGCAAGAGGTTCGGGTAG -3'
(R):5'- ACACGAGTGGCATTGTATACCTC -3'
Posted On 2014-04-24