Mutagenetix > Incidental Mutation

Incidental Mutation 'R7238:Ptpn6'

562979

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

045345-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.481) question?

Stock #

R7238 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

124697670-124715672 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 124698821 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Proline at position 498 (S498P)

Ref Sequence

ENSEMBL: ENSMUSP00000004377 (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

Domain	Start	End	E-Value	Type
low complexity region	18	33	N/A	INTRINSIC
PHB	39	201	1.01e-46	SMART

Predicted Effect

possibly damaging
Transcript: ENSMUST00000004377
AA Change: S498P

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000004377
Gene: ENSMUSG00000004266
AA Change: S498P

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

possibly damaging
Transcript: ENSMUST00000112484
AA Change: S496P

PolyPhen 2 Score 0.712 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000108103
Gene: ENSMUSG00000004266
AA Change: S496P

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

possibly damaging
Transcript: ENSMUST00000171549
AA Change: S498P

PolyPhen 2 Score 0.891 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000129124
Gene: ENSMUSG00000004266
AA Change: S498P

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: ENSMUST00000172690

Predicted Effect

probably benign
Transcript: ENSMUST00000173315

SMART Domains

Protein: ENSMUSP00000134274
Gene: ENSMUSG00000004266

Domain	Start	End	E-Value	Type
SCOP:d1eeoa_	2	38	1e-3	SMART
PDB:3PS5\|A	2	91	2e-41	PDB

Predicted Effect

probably damaging
Transcript: ENSMUST00000174265
AA Change: S457P

PolyPhen 2 Score 0.992 (Sensitivity: 0.70; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000133991
Gene: ENSMUSG00000004266
AA Change: S457P

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

probably benign
Transcript: ENSMUST00000174787

Meta Mutation Damage Score

0.4261

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

97% (104/107)

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: 106 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	T	3: 137,775,712 (GRCm39)	T1634S	probably damaging	Het
Adgrl1	T	A	8: 84,665,693 (GRCm39)	M1460K	probably damaging	Het
Adig	T	A	2: 158,347,773 (GRCm39)	L29Q	unknown	Het
Adnp	T	G	2: 168,025,887 (GRCm39)	K469N	probably damaging	Het
Akap3	A	G	6: 126,842,200 (GRCm39)	D273G	probably benign	Het
Albfm1	A	T	5: 90,727,519 (GRCm39)	Y379F	probably damaging	Het
Ankrd34b	T	C	13: 92,575,139 (GRCm39)	Y124H	possibly damaging	Het
Ap2b1	T	G	11: 83,223,948 (GRCm39)	F221C	possibly damaging	Het
Atp2c2	A	G	8: 120,469,160 (GRCm39)	I358V	possibly damaging	Het
BC051665	G	A	13: 60,930,536 (GRCm39)	T272I	probably benign	Het
Cdan1	G	T	2: 120,560,783 (GRCm39)	A262E	probably benign	Het
Ces1d	C	T	8: 93,904,763 (GRCm39)	V326I	probably benign	Het
Chd3	T	C	11: 69,254,873 (GRCm39)	R156G	probably benign	Het
Clip1	C	T	5: 123,751,328 (GRCm39)	E818K		Het
Col6a4	C	T	9: 105,877,519 (GRCm39)	V2153M	probably damaging	Het
Crlf3	T	C	11: 79,947,351 (GRCm39)	N296D	possibly damaging	Het
Cstdc6	C	T	16: 36,142,193 (GRCm39)	G61D	probably benign	Het
D130052B06Rik	A	G	11: 33,573,594 (GRCm39)	I109V	probably benign	Het
Dcaf5	G	T	12: 80,385,483 (GRCm39)	T881K	probably benign	Het
Dennd4a	C	A	9: 64,769,238 (GRCm39)	T408K	probably damaging	Het
Dnaaf9	C	A	2: 130,648,708 (GRCm39)	R258L	unknown	Het
Dnah2	A	G	11: 69,349,972 (GRCm39)		probably null	Het
Eif1ad8	A	T	12: 87,564,006 (GRCm39)	K114*	probably null	Het
Eif2ak2	C	T	17: 79,173,760 (GRCm39)	V273I	probably benign	Het
Elac1	C	T	18: 73,872,359 (GRCm39)	G212D	probably damaging	Het
Ercc6l2	A	G	13: 64,013,798 (GRCm39)	D623G	probably damaging	Het
Exo1	T	C	1: 175,716,413 (GRCm39)	F177L	probably damaging	Het
Fat4	A	G	3: 38,944,562 (GRCm39)	T1152A	probably benign	Het
Fbxl12	G	T	9: 20,529,709 (GRCm39)		probably null	Het
Fbxo43	T	C	15: 36,151,971 (GRCm39)	Y582C	probably damaging	Het
Fsip2	T	A	2: 82,812,484 (GRCm39)	N2934K	possibly damaging	Het
Gna12	A	G	5: 140,815,847 (GRCm39)	S69P	probably damaging	Het
Gpatch8	C	A	11: 102,369,354 (GRCm39)	G1395C	probably damaging	Het
Gpr137c	A	G	14: 45,516,148 (GRCm39)	Y294C	probably damaging	Het
Greb1	A	G	12: 16,724,673 (GRCm39)	S1834P	probably damaging	Het
Grin2b	T	C	6: 135,757,249 (GRCm39)	D404G	probably damaging	Het
Hectd2	A	T	19: 36,574,478 (GRCm39)	N236I	probably damaging	Het
Hhip	C	T	8: 80,713,641 (GRCm39)	V562I	probably benign	Het
Hipk2	G	T	6: 38,692,992 (GRCm39)	T867N	probably benign	Het
Hmgcl	T	C	4: 135,689,424 (GRCm39)	V294A	possibly damaging	Het
Hnrnpl	T	A	7: 28,513,400 (GRCm39)	F158I		Het
Hspa5	T	C	2: 34,662,383 (GRCm39)	V17A	unknown	Het
Hspg2	T	C	4: 137,235,704 (GRCm39)	V168A	probably damaging	Het
Idh1	A	G	1: 65,205,284 (GRCm39)	F227S	probably damaging	Het
Iigp1c	A	G	18: 60,379,355 (GRCm39)	S297G	possibly damaging	Het
Immp2l	T	C	12: 41,160,915 (GRCm39)	V71A	possibly damaging	Het
Iqce	G	A	5: 140,675,713 (GRCm39)	R193*	probably null	Het
Kcnq5	T	C	1: 21,472,526 (GRCm39)	D907G	probably benign	Het
Krt17	T	A	11: 100,148,613 (GRCm39)	T306S	probably benign	Het
Lhx3	T	C	2: 26,093,009 (GRCm39)	D149G	probably damaging	Het
Lrrc73	G	A	17: 46,565,488 (GRCm39)	R73H	probably damaging	Het
Mgat5b	T	C	11: 116,875,809 (GRCm39)	S678P	probably benign	Het
Mink1	T	C	11: 70,502,305 (GRCm39)		probably null	Het
Mroh5	T	G	15: 73,663,278 (GRCm39)		probably null	Het
Muc5ac	T	A	7: 141,363,254 (GRCm39)	H2188Q	unknown	Het
Muc5ac	G	C	7: 141,363,424 (GRCm39)		probably benign	Het
Musk	G	A	4: 58,344,312 (GRCm39)	G305D	probably benign	Het
Mx1	A	G	16: 97,249,496 (GRCm39)	I347T	unknown	Het
Mybbp1a	G	T	11: 72,334,338 (GRCm39)	V198F	probably damaging	Het
Mycbp2	A	G	14: 103,393,733 (GRCm39)	S2943P	probably damaging	Het
Myo18a	G	A	11: 77,733,059 (GRCm39)	R1363K	probably damaging	Het
Nav3	T	A	10: 109,689,185 (GRCm39)	D364V	possibly damaging	Het
Or13g1	T	C	7: 85,955,799 (GRCm39)	H174R	probably damaging	Het
Or14j6	T	C	17: 38,215,328 (GRCm39)	L297S	probably benign	Het
Or1e26	A	T	11: 73,480,561 (GRCm39)	M1K	probably null	Het
Or1j13	T	A	2: 36,369,726 (GRCm39)	N139Y	possibly damaging	Het
Or5k15	T	A	16: 58,710,252 (GRCm39)	E110D	probably damaging	Het
Pecr	T	C	1: 72,298,592 (GRCm39)	D276G	probably damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 110,350,827 (GRCm39)		probably benign	Het
Ppp1cb	A	T	5: 32,648,376 (GRCm39)	T320S	probably benign	Het
Ppp1r9a	G	T	6: 5,159,716 (GRCm39)	K1084N	probably damaging	Het
Prdm2	A	G	4: 142,862,391 (GRCm39)	S300P	probably benign	Het
Prkg1	C	T	19: 30,602,090 (GRCm39)	V389I	probably damaging	Het
Psg25	C	T	7: 18,266,127 (GRCm39)		probably benign	Het
Pus3	A	G	9: 35,477,965 (GRCm39)	H399R	probably benign	Het
Pus7	T	C	5: 23,983,450 (GRCm39)	T6A	probably benign	Het
Rnf169	A	G	7: 99,574,954 (GRCm39)	V547A	probably benign	Het
Rsf1	GGCGGCGGC	GGCGGCGGCCGCGGCGGC	7: 97,229,128 (GRCm39)		probably benign	Het
Ryr1	C	T	7: 28,794,807 (GRCm39)	D1194N	probably benign	Het
Scn5a	T	C	9: 119,320,610 (GRCm39)	M1490V	possibly damaging	Het
Sec23b	A	G	2: 144,432,258 (GRCm39)	D756G	possibly damaging	Het
Selenoo	T	A	15: 88,973,427 (GRCm39)	M39K	probably benign	Het
Septin8	T	G	11: 53,427,519 (GRCm39)	V246G	possibly damaging	Het
Serpina3k	T	A	12: 104,309,367 (GRCm39)	N270K	probably damaging	Het
Setd5	G	A	6: 113,098,091 (GRCm39)	R710H	probably damaging	Het
Sirt4	A	T	5: 115,621,049 (GRCm39)	I41N	possibly damaging	Het
Slc26a9	T	A	1: 131,686,556 (GRCm39)	Y425*	probably null	Het
Slc4a9	A	G	18: 36,662,773 (GRCm39)	E176G	probably benign	Het
Speer1m	T	C	5: 11,970,712 (GRCm39)	I127T		Het
Spidr	A	T	16: 15,784,680 (GRCm39)	W463R	probably benign	Het
Tenm4	G	A	7: 96,202,703 (GRCm39)	R106H	probably benign	Het
Tmcc1	G	A	6: 116,111,198 (GRCm39)	Q28*	probably null	Het
Tmem52b	A	G	6: 129,493,651 (GRCm39)	E88G	probably damaging	Het
Trpc7	A	T	13: 56,974,710 (GRCm39)	I402K	probably benign	Het
Tshz3	T	C	7: 36,469,522 (GRCm39)	Y504H	probably damaging	Het
Ttn	T	C	2: 76,542,549 (GRCm39)	E33479G	possibly damaging	Het
Ttn	G	A	2: 76,711,672 (GRCm39)	R8290C	unknown	Het
Urb1	T	C	16: 90,549,003 (GRCm39)	D2235G	possibly damaging	Het
Usp10	T	C	8: 120,668,283 (GRCm39)	F195L	probably benign	Het
Vmn1r31	A	T	6: 58,449,858 (GRCm39)	F2L		Het
Vmn2r109	C	T	17: 20,761,336 (GRCm39)	V674M	probably damaging	Het
Vmn2r12	G	A	5: 109,245,655 (GRCm39)	P26S	possibly damaging	Het
Vmn2r61	T	A	7: 41,916,629 (GRCm39)	M414K	possibly damaging	Het
Yipf3	T	C	17: 46,562,585 (GRCm39)	V330A	probably benign	Het
Zic4	A	T	9: 91,261,450 (GRCm39)	H235L	probably benign	Het
Zxdc	T	A	6: 90,346,642 (GRCm39)	W16R	unknown	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
R1900:Ptpn6	UTSW	6	124,705,896 (GRCm39)	missense	probably benign	0.15
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
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'- CGTGATATTCCCATACTCCGAC -3'
(R):5'- TGGAAAGCATCTCCACCAAG -3'

Sequencing Primer
(F):5'- CTTCTGGGACTGTGGGCAAAG -3'
(R):5'- ACCAAGGGTGAGGAGCCC -3'

Posted On

2019-06-26