Mutagenetix > Incidental Mutation

Incidental Mutation 'R1900:Ptpn6'

214187

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

039920-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.489) question?

Stock #

R1900 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

124697670-124715672 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 124705896 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 83 (S83P)

Ref Sequence

ENSEMBL: ENSMUSP00000133991 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000004377] [ENSMUST00000112484] [ENSMUST00000171549] [ENSMUST00000174265] [ENSMUST00000173647] [ENSMUST00000174787]

AlphaFold

P29351

Predicted Effect

probably benign
Transcript: ENSMUST00000004377
AA Change: S124P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000004377
Gene: ENSMUSG00000004266
AA Change: S124P

Domain	Start	End	E-Value	Type
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: ENSMUST00000112484
AA Change: S122P

PolyPhen 2 Score 0.014 (Sensitivity: 0.96; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000108103
Gene: ENSMUSG00000004266
AA Change: S122P

Domain	Start	End	E-Value	Type
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

probably benign
Transcript: ENSMUST00000171549
AA Change: S124P

PolyPhen 2 Score 0.011 (Sensitivity: 0.96; Specificity: 0.78)

SMART Domains

Protein: ENSMUSP00000129124
Gene: ENSMUSG00000004266
AA Change: S124P

Domain	Start	End	E-Value	Type
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: ENSMUST00000172613

Predicted Effect

probably benign
Transcript: ENSMUST00000172690

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000172770

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000173228

Predicted Effect

probably benign
Transcript: ENSMUST00000174265
AA Change: S83P

PolyPhen 2 Score 0.148 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000133991
Gene: ENSMUSG00000004266
AA Change: S83P

Domain	Start	End	E-Value	Type
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: ENSMUST00000174861

Predicted Effect

probably benign
Transcript: ENSMUST00000173647

SMART Domains

Protein: ENSMUSP00000133747
Gene: ENSMUSG00000004266

Domain	Start	End	E-Value	Type
SH2	2	64	2.35e-6	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000174787

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.5%
20x: 93.0%

Validation Efficiency

96% (100/104)

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: 104 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
6330409D20Rik	T	C	2: 32,630,559 (GRCm39)		probably benign	Het
Ago4	T	C	4: 126,410,729 (GRCm39)	I221V	probably benign	Het
Ankfy1	C	T	11: 72,645,233 (GRCm39)	Q771*	probably null	Het
Ankrd50	T	C	3: 38,509,536 (GRCm39)	T944A	probably damaging	Het
Armh4	T	C	14: 50,008,040 (GRCm39)	T478A	probably damaging	Het
AU040320	A	C	4: 126,747,073 (GRCm39)		probably null	Het
Axdnd1	A	G	1: 156,208,344 (GRCm39)		probably null	Het
Cdadc1	A	T	14: 59,823,981 (GRCm39)	D170E	probably damaging	Het
Cep164	C	A	9: 45,721,123 (GRCm39)	R93L	probably damaging	Het
Cep250	T	C	2: 155,827,294 (GRCm39)		probably null	Het
Cfdp1	G	A	8: 112,495,361 (GRCm39)	R286*	probably null	Het
Chrdl2	A	G	7: 99,682,871 (GRCm39)	I377V	possibly damaging	Het
Cntrob	A	T	11: 69,198,880 (GRCm39)	S623T	probably benign	Het
Col6a5	C	T	9: 105,808,412 (GRCm39)	G879S	unknown	Het
Cyp2c38	T	A	19: 39,426,756 (GRCm39)	I182F	probably benign	Het
Dennd4a	T	C	9: 64,804,618 (GRCm39)	V1319A	probably damaging	Het
Dysf	T	G	6: 84,016,549 (GRCm39)	V70G	probably damaging	Het
Edn3	A	G	2: 174,603,398 (GRCm39)	T49A	possibly damaging	Het
Elac1	C	G	18: 73,872,316 (GRCm39)	L226F	probably damaging	Het
Eps8l3	A	G	3: 107,798,268 (GRCm39)	D445G	probably benign	Het
Fgf11	G	T	11: 69,692,279 (GRCm39)	T58K	probably benign	Het
Fstl5	T	A	3: 76,615,467 (GRCm39)	W843R	probably damaging	Het
Fyb2	A	G	4: 104,802,652 (GRCm39)	R185G	probably benign	Het
Gal3st2c	G	A	1: 93,936,766 (GRCm39)	R237H	probably damaging	Het
Galnt15	G	T	14: 31,771,822 (GRCm39)	R289L	probably damaging	Het
Garin4	T	A	1: 190,896,631 (GRCm39)	K4M	possibly damaging	Het
Gdf5	T	A	2: 155,784,001 (GRCm39)	D317V	probably damaging	Het
Gm7808	A	G	9: 19,839,410 (GRCm39)		probably benign	Het
Hcn3	T	C	3: 89,055,570 (GRCm39)	E559G	probably benign	Het
Hdlbp	A	T	1: 93,349,959 (GRCm39)		probably benign	Het
Hhip	T	C	8: 80,701,675 (GRCm39)	T620A	probably benign	Het
Hs3st3a1	T	C	11: 64,411,268 (GRCm39)	S269P	probably damaging	Het
Il17ra	A	T	6: 120,454,355 (GRCm39)		probably null	Het
Kif2a	T	C	13: 107,113,503 (GRCm39)	N417S	possibly damaging	Het
Klhl41	T	A	2: 69,504,963 (GRCm39)		probably benign	Het
L3mbtl4	G	T	17: 68,766,800 (GRCm39)	C169F	probably damaging	Het
Lap3	T	C	5: 45,669,252 (GRCm39)	F467S	probably damaging	Het
Lpar6	A	T	14: 73,476,579 (GRCm39)	Y180F	probably benign	Het
Lrig3	T	C	10: 125,838,262 (GRCm39)		probably benign	Het
Ltbp2	A	T	12: 84,877,432 (GRCm39)	S378T	probably damaging	Het
Ltf	T	C	9: 110,851,913 (GRCm39)	F117L	possibly damaging	Het
Med16	T	C	10: 79,734,765 (GRCm39)	E533G	probably damaging	Het
Meltf	T	C	16: 31,700,787 (GRCm39)		probably null	Het
Mphosph10	C	T	7: 64,030,776 (GRCm39)	E488K	possibly damaging	Het
Mroh1	A	G	15: 76,317,585 (GRCm39)	T812A	probably benign	Het
Mto1	T	C	9: 78,368,799 (GRCm39)		probably benign	Het
Ndst1	A	T	18: 60,845,793 (GRCm39)		probably null	Het
Ndst4	T	A	3: 125,491,544 (GRCm39)		probably null	Het
Nhlh1	A	T	1: 171,881,608 (GRCm39)	I86N	probably damaging	Het
Nme9	A	C	9: 99,341,827 (GRCm39)	D59A	probably damaging	Het
Nox4	A	T	7: 87,010,004 (GRCm39)	R402*	probably null	Het
Npr1	T	C	3: 90,369,495 (GRCm39)	D410G	probably damaging	Het
Nrip1	T	A	16: 76,088,927 (GRCm39)	T877S	probably benign	Het
Nsd2	A	G	5: 34,003,513 (GRCm39)	N221S	probably benign	Het
Ophn1	A	T	X: 97,769,665 (GRCm39)	Y181*	probably null	Het
Or13a28	A	T	7: 140,218,505 (GRCm39)	D297V	probably damaging	Het
Or1e17	C	A	11: 73,831,486 (GRCm39)	P138Q	possibly damaging	Het
Or4c123	T	C	2: 89,127,014 (GRCm39)	N200S	probably damaging	Het
Or51ac3	A	T	7: 103,213,814 (GRCm39)	L224*	probably null	Het
Or51f5	A	T	7: 102,424,538 (GRCm39)	H269L	probably benign	Het
Or5b109	T	A	19: 13,212,277 (GRCm39)	I221K	possibly damaging	Het
Or8c10	A	T	9: 38,279,360 (GRCm39)	I173L	probably benign	Het
Parp1	A	G	1: 180,424,904 (GRCm39)	K819R	probably damaging	Het
Parp9	T	C	16: 35,792,591 (GRCm39)	S829P	probably benign	Het
Pde6c	T	A	19: 38,150,388 (GRCm39)	F511Y	probably damaging	Het
Per3	G	T	4: 151,125,883 (GRCm39)	H145Q	probably damaging	Het
Pglyrp1	C	T	7: 18,624,151 (GRCm39)	R145W	probably damaging	Het
Piezo1	T	C	8: 123,209,384 (GRCm39)		probably benign	Het
Plb1	T	C	5: 32,444,191 (GRCm39)	I312T	probably benign	Het
Plin3	T	A	17: 56,586,824 (GRCm39)	T408S	possibly damaging	Het
Polr2a	A	T	11: 69,634,772 (GRCm39)	I636N	probably damaging	Het
Pramel51	A	C	12: 88,144,030 (GRCm39)	L261R	probably benign	Het
Prb1b	A	T	6: 132,291,661 (GRCm39)	L11Q	unknown	Het
Prex2	G	T	1: 11,232,590 (GRCm39)	E886*	probably null	Het
Proca1	A	T	11: 78,095,847 (GRCm39)	I73F	probably damaging	Het
Rtp1	G	T	16: 23,248,049 (GRCm39)	V41L	probably benign	Het
Scn4a	A	G	11: 106,218,359 (GRCm39)	I1035T	probably damaging	Het
Sell	A	T	1: 163,892,907 (GRCm39)	Y41F	probably damaging	Het
Serping1	C	T	2: 84,601,793 (GRCm39)	V226M	probably damaging	Het
Sf3b1	A	T	1: 55,037,347 (GRCm39)	D856E	possibly damaging	Het
Sfmbt1	T	A	14: 30,524,524 (GRCm39)	Y503N	probably damaging	Het
Slc16a1	T	A	3: 104,560,880 (GRCm39)	V395D	probably damaging	Het
Slc22a7	A	T	17: 46,749,157 (GRCm39)	D53E	probably benign	Het
Slc35b3	A	G	13: 39,144,587 (GRCm39)		probably null	Het
Slc6a1	T	C	6: 114,288,815 (GRCm39)	M274T	possibly damaging	Het
Slco1a5	A	G	6: 142,187,789 (GRCm39)	S517P	probably benign	Het
Smo	A	G	6: 29,736,055 (GRCm39)	R16G	unknown	Het
Srebf1	A	G	11: 60,094,312 (GRCm39)	L601P	probably damaging	Het
Sspo	A	G	6: 48,436,284 (GRCm39)	I1086M	probably benign	Het
Tas2r106	A	T	6: 131,655,373 (GRCm39)	N159K	probably damaging	Het
Thsd1	G	A	8: 22,742,334 (GRCm39)		probably benign	Het
Tmeff1	T	C	4: 48,658,938 (GRCm39)		probably benign	Het
Tmem140	G	A	6: 34,849,838 (GRCm39)	C118Y	possibly damaging	Het
Tmem168	A	G	6: 13,583,070 (GRCm39)	C220R	probably benign	Het
Tox2	A	T	2: 163,118,087 (GRCm39)	N129Y	probably damaging	Het
Trappc12	C	T	12: 28,796,984 (GRCm39)	E183K	probably damaging	Het
Unc50	A	G	1: 37,477,880 (GRCm39)	Y254C	probably damaging	Het
Unk	T	G	11: 115,949,907 (GRCm39)	D691E	probably benign	Het
Uox	T	A	3: 146,316,134 (GRCm39)	V23D	probably damaging	Het
Vps13d	A	G	4: 144,853,176 (GRCm39)	C2313R	probably benign	Het
Zfp804b	T	A	5: 6,819,283 (GRCm39)	H1260L	probably damaging	Het
Zfyve26	A	G	12: 79,311,125 (GRCm39)	L147P	probably damaging	Het
Zmynd10	A	T	9: 107,427,236 (GRCm39)	Q288L	probably benign	Het
Zzef1	T	A	11: 72,739,540 (GRCm39)	D662E	probably damaging	Het

Other mutations in Ptpn6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH 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
R2047:Ptpn6	UTSW	6	124,698,752 (GRCm39)	missense	probably benign	0.42
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'- AAGTCCACTGAAGCTCCAGC -3'
(R):5'- GCTGGGGTAATAGCACAAAGTC -3'

Sequencing Primer
(F):5'- CTCCAGCGTGAGGCCAC -3'
(R):5'- AGCACAAAGTCTATCTTTTTCCTCAC -3'

Posted On

2014-07-14