Incidental Mutation 'R2047:Ptpn6'
ID 222095
Institutional Source Beutler Lab
Gene Symbol Ptpn6
Ensembl Gene ENSMUSG00000004266
Gene Name protein tyrosine phosphatase, non-receptor type 6
Synonyms Hcph, SHP-1, hcp, Ptp1C
MMRRC Submission 040054-MU
Accession Numbers
Essential gene? Possibly non essential (E-score: 0.489) question?
Stock # R2047 (G1)
Quality Score 225
Status Validated
Chromosome 6
Chromosomal Location 124697670-124715672 bp(-) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) T to C at 124698752 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Threonine to Alanine at position 480 (T480A)
Ref Sequence ENSEMBL: ENSMUSP00000133991 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000004375] [ENSMUST00000004377] [ENSMUST00000112484] [ENSMUST00000171549] [ENSMUST00000174265] [ENSMUST00000174787]
AlphaFold P29351
Predicted Effect probably benign
Transcript: ENSMUST00000004375
SMART Domains Protein: ENSMUSP00000004375
Gene: ENSMUSG00000004264

DomainStartEndE-ValueType
low complexity region 18 33 N/A INTRINSIC
PHB 39 201 1.01e-46 SMART
Predicted Effect probably benign
Transcript: ENSMUST00000004377
AA Change: T521A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000004377
Gene: ENSMUSG00000004266
AA Change: T521A

DomainStartEndE-ValueType
SH2 4 87 1.43e-28 SMART
SH2 110 202 1.45e-29 SMART
PTPc 245 519 7.51e-131 SMART
low complexity region 571 581 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000083528
Predicted Effect noncoding transcript
Transcript: ENSMUST00000083540
Predicted Effect probably benign
Transcript: ENSMUST00000112484
AA Change: T519A

PolyPhen 2 Score 0.001 (Sensitivity: 0.99; Specificity: 0.15)
SMART Domains Protein: ENSMUSP00000108103
Gene: ENSMUSG00000004266
AA Change: T519A

DomainStartEndE-ValueType
SH2 2 85 4.05e-28 SMART
SH2 108 200 1.45e-29 SMART
PTPc 243 517 7.51e-131 SMART
low complexity region 569 579 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143000
Predicted Effect probably benign
Transcript: ENSMUST00000171549
AA Change: T521A

PolyPhen 2 Score 0.003 (Sensitivity: 0.98; Specificity: 0.44)
SMART Domains Protein: ENSMUSP00000129124
Gene: ENSMUSG00000004266
AA Change: T521A

DomainStartEndE-ValueType
SH2 4 87 1.43e-28 SMART
SH2 110 202 1.45e-29 SMART
PTPc 245 519 7.51e-131 SMART
low complexity region 571 581 N/A INTRINSIC
Predicted Effect probably benign
Transcript: ENSMUST00000173315
AA Change: T18A

PolyPhen 2 Score 0.376 (Sensitivity: 0.90; Specificity: 0.89)
SMART Domains Protein: ENSMUSP00000134274
Gene: ENSMUSG00000004266
AA Change: T18A

DomainStartEndE-ValueType
SCOP:d1eeoa_ 2 38 1e-3 SMART
PDB:3PS5|A 2 91 2e-41 PDB
Predicted Effect probably benign
Transcript: ENSMUST00000174265
AA Change: T480A

PolyPhen 2 Score 0.423 (Sensitivity: 0.89; Specificity: 0.90)
SMART Domains Protein: ENSMUSP00000133991
Gene: ENSMUSG00000004266
AA Change: T480A

DomainStartEndE-ValueType
Pfam:SH2 1 40 3.5e-6 PFAM
SH2 69 161 1.45e-29 SMART
PTPc 204 478 7.51e-131 SMART
low complexity region 530 540 N/A INTRINSIC
Predicted Effect noncoding transcript
Transcript: ENSMUST00000145447
Predicted Effect noncoding transcript
Transcript: ENSMUST00000143765
Predicted Effect noncoding transcript
Transcript: ENSMUST00000189387
Predicted Effect probably benign
Transcript: ENSMUST00000174787
Predicted Effect probably benign
Transcript: ENSMUST00000172690
Meta Mutation Damage Score 0.0854 question?
Coding Region Coverage
  • 1x: 99.2%
  • 3x: 98.5%
  • 10x: 97.0%
  • 20x: 94.4%
Validation Efficiency 100% (57/57)
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 protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. N-terminal part of this PTP contains two tandem Src homolog (SH2) domains, which act as protein phospho-tyrosine binding domains, and mediate the interaction of this PTP with its substrates. This PTP is expressed primarily in hematopoietic cells, and functions as an important regulator of multiple signaling pathways in hematopoietic cells. This PTP has been shown to interact with, and dephosphorylate a wide spectrum of phospho-proteins involved in hematopoietic cell signaling. Multiple alternatively spliced variants of this gene, which encode distinct isoforms, have been reported. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutants are immunodeficient and autoimmune and exhibit neutrophilic skin lesions that disrupt hair follicles and give the motheaten appearance. Alleles vary in severity, with death occurring at 6-9 weeks postnatally due to severe pneumonitis. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 56 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
4933402N03Rik A G 7: 130,747,836 (GRCm39) F52S probably damaging Het
Acot12 T C 13: 91,931,122 (GRCm39) S457P probably damaging Het
Adcy5 G A 16: 35,110,478 (GRCm39) V882M possibly damaging Het
Ahnak A G 19: 8,991,664 (GRCm39) D4316G possibly damaging Het
Aldh1l2 G A 10: 83,342,607 (GRCm39) A401V probably damaging Het
Apol7e A G 15: 77,601,810 (GRCm39) H136R probably benign Het
Arl5a A G 2: 52,302,072 (GRCm39) probably null Het
Asns G T 6: 7,680,093 (GRCm39) A341E probably damaging Het
C7 A G 15: 5,075,143 (GRCm39) L183P probably damaging Het
Cacng2 C T 15: 78,003,037 (GRCm39) A19T probably damaging Het
Ccdc121rt2 A G 5: 112,598,575 (GRCm39) N374S probably benign Het
Ccr4 A G 9: 114,321,633 (GRCm39) F144S probably damaging Het
Ckap2 A G 8: 22,658,763 (GRCm39) V660A probably benign Het
Cramp1 A T 17: 25,222,189 (GRCm39) Y176* probably null Het
Dgki A G 6: 36,890,581 (GRCm39) S922P possibly damaging Het
Drd5 C T 5: 38,477,679 (GRCm39) S224L probably damaging Het
Ei24 T C 9: 36,691,459 (GRCm39) K341E probably benign Het
Eno2 A T 6: 124,744,659 (GRCm39) probably benign Het
Epb41l4a T C 18: 33,961,259 (GRCm39) N425S probably benign Het
F13b T G 1: 139,435,961 (GRCm39) C256G probably damaging Het
Gp6 A T 7: 4,376,270 (GRCm39) probably benign Het
H2-Q7 A T 17: 35,659,123 (GRCm39) R191S probably damaging Het
Ivns1abp T A 1: 151,227,382 (GRCm39) S63R possibly damaging Het
Kcnj16 A G 11: 110,915,946 (GRCm39) probably null Het
Lpcat4 T C 2: 112,075,142 (GRCm39) probably null Het
Lrrc14b T C 13: 74,511,561 (GRCm39) K173R probably benign Het
Maml3 C A 3: 51,597,866 (GRCm39) R939S probably damaging Het
Mrgpra2b C T 7: 47,113,908 (GRCm39) V249I probably benign Het
Mrpl46 T A 7: 78,431,312 (GRCm39) Y82F probably damaging Het
Mthfs T A 9: 89,097,356 (GRCm39) I71N probably damaging Het
Nectin4 T C 1: 171,212,720 (GRCm39) V351A possibly damaging Het
Npas3 T C 12: 54,115,612 (GRCm39) F827L probably damaging Het
Nrp1 G A 8: 129,224,577 (GRCm39) probably benign Het
Ocln C A 13: 100,671,632 (GRCm39) A242S probably damaging Het
Or10ad1c T A 15: 98,084,920 (GRCm39) T253S probably damaging Het
Or13g1 G A 7: 85,956,012 (GRCm39) T103I probably damaging Het
Or5d37 A T 2: 87,924,237 (GRCm39) N14K probably benign Het
Pappa T C 4: 65,149,378 (GRCm39) probably benign Het
Pycr1 A T 11: 120,532,512 (GRCm39) D168E possibly damaging Het
Rnf6 T C 5: 146,148,674 (GRCm39) T126A probably damaging Het
Slc25a39 G A 11: 102,296,657 (GRCm39) probably benign Het
Slc35f4 G T 14: 49,541,029 (GRCm39) probably benign Het
Sppl2a C T 2: 126,768,772 (GRCm39) A112T probably damaging Het
Sptbn1 A C 11: 30,088,360 (GRCm39) probably benign Het
Sqle T C 15: 59,197,907 (GRCm39) Y376H probably benign Het
Terb1 A T 8: 105,212,094 (GRCm39) Y296N probably damaging Het
Ttbk2 T C 2: 120,579,397 (GRCm39) H506R probably damaging Het
Ttn T C 2: 76,737,879 (GRCm39) D4220G probably benign Het
Tub A G 7: 108,625,939 (GRCm39) D230G probably benign Het
Ube2d3 T A 3: 135,170,967 (GRCm39) I137K probably benign Het
Vldlr G T 19: 27,212,238 (GRCm39) C84F probably damaging Het
Vmn1r54 A T 6: 90,246,970 (GRCm39) I295F probably damaging Het
Vmn2r56 A G 7: 12,466,918 (GRCm39) S39P probably damaging Het
Zfp358 A G 8: 3,545,934 (GRCm39) H172R probably damaging Het
Zfp619 T C 7: 39,187,062 (GRCm39) C1031R probably damaging Het
Zfp777 A G 6: 48,021,280 (GRCm39) I114T probably benign Het
Other mutations in Ptpn6
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL00710:Ptpn6 APN 6 124,709,319 (GRCm39) splice site probably null
IGL01490:Ptpn6 APN 6 124,705,307 (GRCm39) missense probably damaging 1.00
IGL01865:Ptpn6 APN 6 124,709,428 (GRCm39) missense probably damaging 1.00
IGL02017:Ptpn6 APN 6 124,709,449 (GRCm39) missense probably damaging 0.98
IGL02272:Ptpn6 APN 6 124,698,171 (GRCm39) missense probably damaging 0.99
IGL02276:Ptpn6 APN 6 124,705,828 (GRCm39) missense probably null 1.00
IGL02556:Ptpn6 APN 6 124,705,623 (GRCm39) missense probably benign 0.00
candle UTSW 6 124,705,382 (GRCm39) missense probably damaging 1.00
caterpillar UTSW 6 124,701,947 (GRCm39) missense probably benign
farfalla_notturna UTSW 6 124,709,398 (GRCm39) missense probably damaging 1.00
Flutterby UTSW 6 124,698,821 (GRCm39) missense possibly damaging 0.89
Hawk UTSW 6 124,705,748 (GRCm39) missense probably damaging 1.00
Lepidopteran UTSW 6 124,705,135 (GRCm39) missense probably damaging 1.00
Malachite UTSW 6 124,705,614 (GRCm39) missense possibly damaging 0.84
Moth UTSW 6 124,705,135 (GRCm39) missense possibly damaging 0.89
Naphthalene UTSW 6 124,698,752 (GRCm39) missense probably benign 0.42
spin UTSW 6 124,705,522 (GRCm39) missense probably damaging 1.00
spin2 UTSW 6 124,709,332 (GRCm39) missense probably damaging 1.00
Vermeil UTSW 6 124,709,913 (GRCm39) missense probably benign 0.10
R0183:Ptpn6 UTSW 6 124,705,914 (GRCm39) missense probably damaging 1.00
R0254:Ptpn6 UTSW 6 124,705,113 (GRCm39) missense probably damaging 1.00
R0636:Ptpn6 UTSW 6 124,702,242 (GRCm39) missense probably benign
R0835:Ptpn6 UTSW 6 124,704,499 (GRCm39) critical splice acceptor site probably null
R1383:Ptpn6 UTSW 6 124,698,856 (GRCm39) missense probably damaging 1.00
R1638:Ptpn6 UTSW 6 124,698,148 (GRCm39) missense probably benign
R1900:Ptpn6 UTSW 6 124,705,896 (GRCm39) missense probably benign 0.15
R2143:Ptpn6 UTSW 6 124,701,947 (GRCm39) missense probably benign 0.01
R3907:Ptpn6 UTSW 6 124,702,239 (GRCm39) missense possibly damaging 0.86
R4082:Ptpn6 UTSW 6 124,705,382 (GRCm39) missense probably damaging 1.00
R4382:Ptpn6 UTSW 6 124,704,361 (GRCm39) missense possibly damaging 0.86
R5319:Ptpn6 UTSW 6 124,709,913 (GRCm39) missense probably benign 0.10
R5807:Ptpn6 UTSW 6 124,701,947 (GRCm39) missense probably benign
R5878:Ptpn6 UTSW 6 124,705,748 (GRCm39) missense probably damaging 1.00
R6056:Ptpn6 UTSW 6 124,709,398 (GRCm39) missense probably damaging 1.00
R6374:Ptpn6 UTSW 6 124,709,532 (GRCm39) splice site probably null
R7238:Ptpn6 UTSW 6 124,698,821 (GRCm39) missense possibly damaging 0.89
R7381:Ptpn6 UTSW 6 124,705,135 (GRCm39) missense probably damaging 1.00
R7935:Ptpn6 UTSW 6 124,709,425 (GRCm39) missense possibly damaging 0.93
R8297:Ptpn6 UTSW 6 124,705,614 (GRCm39) missense possibly damaging 0.84
R8863:Ptpn6 UTSW 6 124,709,309 (GRCm39) missense probably damaging 1.00
R9160:Ptpn6 UTSW 6 124,705,135 (GRCm39) missense possibly damaging 0.89
R9176:Ptpn6 UTSW 6 124,702,249 (GRCm39) missense probably benign
R9448:Ptpn6 UTSW 6 124,709,771 (GRCm39) missense probably damaging 1.00
R9594:Ptpn6 UTSW 6 124,704,728 (GRCm39) missense probably benign 0.04
R9756:Ptpn6 UTSW 6 124,705,592 (GRCm39) missense probably damaging 1.00
Z1176:Ptpn6 UTSW 6 124,702,039 (GRCm39) nonsense probably null
Predicted Primers PCR Primer
(F):5'- AGCGGGAGGGTACGTGATATTC -3'
(R):5'- TGGAAAGCATCTCCACCAAG -3'

Sequencing Primer
(F):5'- GAGGGTACGTGATATTCCCATACTC -3'
(R):5'- GGGCAAGCCATCCCTTG -3'
Posted On 2014-08-25