Mutagenetix > Incidental Mutation

Incidental Mutation 'R1954:Ptpn23'

217573

Institutional Source

Beutler Lab

Gene Symbol

Ptpn23

Ensembl Gene

ENSMUSG00000036057

Gene Name

protein tyrosine phosphatase, non-receptor type 23

Synonyms

PTP-TD14

MMRRC Submission

039968-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R1954 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

110214152-110237278 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 110215393 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Lysine at position 1422 (N1422K)

Ref Sequence

ENSEMBL: ENSMUSP00000039580 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040021] [ENSMUST00000098350]

AlphaFold

Q6PB44

PDB Structure

MONA SH3C IN COMPLEX [X-RAY DIFFRACTION]

Predicted Effect

probably damaging
Transcript: ENSMUST00000040021
AA Change: N1422K

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000039580
Gene: ENSMUSG00000036057
AA Change: N1422K

Domain	Start	End	E-Value	Type
BRO1	8	384	5.94e-159	SMART
Pfam:ALIX_LYPXL_bnd	416	704	1.4e-64	PFAM
low complexity region	715	728	N/A	INTRINSIC
low complexity region	774	785	N/A	INTRINSIC
low complexity region	849	858	N/A	INTRINSIC
low complexity region	905	928	N/A	INTRINSIC
internal_repeat_1	929	942	8.2e-5	PROSPERO
internal_repeat_1	943	956	8.2e-5	PROSPERO
low complexity region	977	1018	N/A	INTRINSIC
low complexity region	1040	1061	N/A	INTRINSIC
low complexity region	1088	1106	N/A	INTRINSIC
low complexity region	1128	1160	N/A	INTRINSIC
low complexity region	1185	1200	N/A	INTRINSIC
low complexity region	1225	1235	N/A	INTRINSIC
PTPc	1246	1510	1.28e-92	SMART
low complexity region	1576	1587	N/A	INTRINSIC
low complexity region	1589	1643	N/A	INTRINSIC
Blast:PTPc	1644	1673	9e-8	BLAST
low complexity region	1675	1689	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000098350

SMART Domains

Protein: ENSMUSP00000095953
Gene: ENSMUSG00000032485

Domain	Start	End	E-Value	Type
transmembrane domain	20	42	N/A	INTRINSIC
low complexity region	43	54	N/A	INTRINSIC
low complexity region	153	165	N/A	INTRINSIC
Pfam:Patched	279	504	4.7e-24	PFAM
Pfam:Sterol-sensing	308	459	7.6e-54	PFAM
transmembrane domain	515	534	N/A	INTRINSIC
transmembrane domain	711	733	N/A	INTRINSIC
low complexity region	741	751	N/A	INTRINSIC
WD40	765	802	1.79e-1	SMART
low complexity region	847	865	N/A	INTRINSIC
low complexity region	928	944	N/A	INTRINSIC
WD40	953	990	9.86e1	SMART
low complexity region	1050	1060	N/A	INTRINSIC
WD40	1062	1102	4.18e-2	SMART
WD40	1105	1143	5.64e-8	SMART
WD40	1147	1183	2.4e-1	SMART
WD40	1186	1223	2.56e1	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000199254

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000200278

Predicted Effect

probably benign
Transcript: ENSMUST00000200531

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.8%
20x: 94.0%

Validation Efficiency

97% (101/104)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the non-receptor type protein-tyrosine phosphatase family. The encoded protein may be involved in the regulation of small nuclear ribonucleo protein assembly and pre-mRNA splicing by modifying the survival motor neuron (SMN) complex. The encoded protein additionally plays a role in ciliogenesis and is part of endosomal sorting complex required for transport (ESCRT) pathways. This gene may serve a tumor suppressor function. [provided by RefSeq, Jul 2016]
PHENOTYPE: Embryos homozygous for a gene trap allele are significantly growth retarded and fail to reach the E8.5 stage. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adamts15	T	A	9: 30,822,004 (GRCm39)	M478L	probably benign	Het
Akap8l	T	A	17: 32,555,710 (GRCm39)	Y123F	possibly damaging	Het
Anapc4	T	G	5: 53,003,967 (GRCm39)		probably benign	Het
Arap3	A	G	18: 38,115,055 (GRCm39)	V987A	probably damaging	Het
Atp2b4	T	A	1: 133,667,730 (GRCm39)	T105S	probably damaging	Het
Atp6v0d1	A	G	8: 106,292,525 (GRCm39)	L7P	probably damaging	Het
Atp6v1b2	T	C	8: 69,558,555 (GRCm39)	V341A	possibly damaging	Het
Baz2b	C	A	2: 59,799,087 (GRCm39)	A346S	probably benign	Het
Brpf3	G	A	17: 29,025,533 (GRCm39)	S202N	probably benign	Het
Btnl4	T	C	17: 34,691,904 (GRCm39)	K233E	possibly damaging	Het
Capn7	A	G	14: 31,082,107 (GRCm39)	T438A	probably damaging	Het
Cars2	A	T	8: 11,600,286 (GRCm39)	Y68N	probably damaging	Het
Cbx2	G	T	11: 118,919,166 (GRCm39)	G244W	probably damaging	Het
Ccr4	A	T	9: 114,321,753 (GRCm39)	V104D	probably damaging	Het
Cdc5l	T	C	17: 45,737,442 (GRCm39)		probably null	Het
Cep170	A	T	1: 176,583,950 (GRCm39)	C810S	probably benign	Het
Cfap299	A	T	5: 98,714,612 (GRCm39)		probably benign	Het
Clp1	T	C	2: 84,554,395 (GRCm39)	D258G	probably damaging	Het
Clstn3	T	C	6: 124,436,257 (GRCm39)	E164G	possibly damaging	Het
Col28a1	T	C	6: 7,998,516 (GRCm39)	E1131G	probably damaging	Het
Cps1	A	G	1: 67,234,355 (GRCm39)	D914G	possibly damaging	Het
Ctnnal1	C	T	4: 56,817,242 (GRCm39)		probably benign	Het
Cyp2c38	A	G	19: 39,393,131 (GRCm39)	L312P	probably damaging	Het
Cytip	T	C	2: 58,038,265 (GRCm39)	N99D	possibly damaging	Het
Dennd4a	A	T	9: 64,759,749 (GRCm39)	T285S	probably benign	Het
Dhx8	A	G	11: 101,644,105 (GRCm39)	S842G	probably damaging	Het
Disp1	A	T	1: 182,870,107 (GRCm39)	M771K	probably damaging	Het
Dnah17	A	G	11: 117,915,557 (GRCm39)	I4326T	probably damaging	Het
Efcab7	T	C	4: 99,757,887 (GRCm39)	F345L	probably damaging	Het
Erc1	G	T	6: 119,774,266 (GRCm39)	Q230K	probably damaging	Het
Ern1	A	T	11: 106,312,800 (GRCm39)		probably benign	Het
Espl1	T	C	15: 102,206,823 (GRCm39)	Y96H	probably damaging	Het
Fam135a	A	T	1: 24,068,683 (GRCm39)	L533I	probably damaging	Het
Fat2	G	A	11: 55,201,910 (GRCm39)	T388I	probably benign	Het
Galnt1	T	G	18: 24,404,831 (GRCm39)		probably benign	Het
Glmn	A	G	5: 107,720,243 (GRCm39)	F212S	probably damaging	Het
Gm3604	A	T	13: 62,517,025 (GRCm39)	N444K	probably damaging	Het
Gvin-ps5	A	C	7: 105,928,888 (GRCm39)	D336E	probably damaging	Het
H1f2	T	C	13: 23,923,385 (GRCm39)	V185A	unknown	Het
H1f3	A	G	13: 23,739,690 (GRCm39)		probably benign	Het
H2-M10.3	T	C	17: 36,678,390 (GRCm39)	D145G	probably damaging	Het
Hic2	T	A	16: 17,076,857 (GRCm39)	L562Q	probably damaging	Het
Hip1r	G	T	5: 124,139,907 (GRCm39)	E1003D	probably damaging	Het
Hsfy2	C	T	1: 56,676,342 (GRCm39)	C65Y	probably benign	Het
Inpp1	T	C	1: 52,833,788 (GRCm39)	T103A	probably damaging	Het
Ints5	T	C	19: 8,872,260 (GRCm39)	V73A	probably damaging	Het
Iqch	A	T	9: 63,455,298 (GRCm39)	D166E	probably benign	Het
Klhdc3	A	T	17: 46,988,901 (GRCm39)	N96K	probably damaging	Het
Klk1b8	C	T	7: 43,603,272 (GRCm39)		probably benign	Het
Klrb1	T	C	6: 128,700,036 (GRCm39)		probably null	Het
Krt71	C	A	15: 101,643,901 (GRCm39)	G446*	probably null	Het
Lars1	G	A	18: 42,343,115 (GRCm39)	R1101C	probably damaging	Het
Lemd3	G	T	10: 120,814,845 (GRCm39)	S129R	probably damaging	Het
Lrp1b	A	G	2: 40,748,453 (GRCm39)	L3015P	probably damaging	Het
Mdga2	T	C	12: 66,533,482 (GRCm39)		probably benign	Het
Mlst8	A	T	17: 24,696,195 (GRCm39)	I178N	probably damaging	Het
Mon2	A	T	10: 122,874,388 (GRCm39)	I320N	probably damaging	Het
Morc2b	T	C	17: 33,356,464 (GRCm39)	Y436C	probably damaging	Het
Moxd1	T	A	10: 24,155,781 (GRCm39)	M295K	probably benign	Het
Mrps5	T	A	2: 127,438,817 (GRCm39)		probably null	Het
Mtor	C	A	4: 148,552,730 (GRCm39)	S744R	probably damaging	Het
Myo3a	T	A	2: 22,246,037 (GRCm39)	D61E	probably damaging	Het
Nars1	C	T	18: 64,633,635 (GRCm39)	R545Q	probably damaging	Het
Ncoa6	A	G	2: 155,248,741 (GRCm39)	V1521A	possibly damaging	Het
Ndor1	T	C	2: 25,145,305 (GRCm39)	E20G	possibly damaging	Het
Nipsnap3b	T	C	4: 53,017,213 (GRCm39)		probably benign	Het
Notch3	G	T	17: 32,385,652 (GRCm39)	A39E	probably benign	Het
Or1j16	A	G	2: 36,530,227 (GRCm39)	M59V	possibly damaging	Het
Or2a14	T	C	6: 43,130,911 (GRCm39)	I224T	possibly damaging	Het
Or6z3	G	T	7: 6,464,144 (GRCm39)	W212L	probably benign	Het
Otud3	T	C	4: 138,625,343 (GRCm39)	K237R	possibly damaging	Het
Papola	T	A	12: 105,794,532 (GRCm39)		probably null	Het
Parl	T	A	16: 20,121,077 (GRCm39)	M1L	possibly damaging	Het
Parp14	G	T	16: 35,678,671 (GRCm39)	N432K	probably benign	Het
Patz1	T	G	11: 3,241,088 (GRCm39)	S159A	probably damaging	Het
Prpf6	T	G	2: 181,273,870 (GRCm39)	M338R	probably benign	Het
Psd3	A	G	8: 68,149,727 (GRCm39)	L343P	probably damaging	Het
Rab19	A	T	6: 39,361,016 (GRCm39)	T55S	probably benign	Het
Sh3yl1	A	G	12: 30,972,332 (GRCm39)	K34E	possibly damaging	Het
Skint8	T	A	4: 111,807,278 (GRCm39)	F321L	possibly damaging	Het
Slc25a46	A	T	18: 31,733,294 (GRCm39)		probably null	Het
Slc26a3	T	C	12: 31,500,815 (GRCm39)	L184S	probably damaging	Het
Slc39a10	A	T	1: 46,874,334 (GRCm39)	S323T	possibly damaging	Het
Sorbs2	G	T	8: 46,198,775 (GRCm39)	R20L	probably benign	Het
Stk32a	A	T	18: 43,345,090 (GRCm39)	D13V	probably benign	Het
Tab2	T	C	10: 7,795,094 (GRCm39)	T463A	probably damaging	Het
Tenm2	T	A	11: 35,938,374 (GRCm39)	N1433I	possibly damaging	Het
Tmem200c	A	T	17: 69,147,956 (GRCm39)	I180F	probably damaging	Het
Tmem232	G	T	17: 65,791,482 (GRCm39)	H129N	probably benign	Het
Tmem242	T	C	17: 5,489,854 (GRCm39)	T47A	possibly damaging	Het
Ube2d1	A	T	10: 71,120,953 (GRCm39)	M1K	probably null	Het
Ube2frt	A	G	12: 36,140,595 (GRCm39)		probably benign	Het
Uckl1	T	C	2: 181,212,320 (GRCm39)	Q332R	probably benign	Het
Unc5b	T	C	10: 60,605,044 (GRCm39)		probably benign	Het
Vmn2r114	T	C	17: 23,530,086 (GRCm39)	Y107C	probably benign	Het
Vmn2r82	A	T	10: 79,231,890 (GRCm39)	S630C	probably damaging	Het
Wdr25	T	A	12: 108,864,467 (GRCm39)	V204E	probably damaging	Het
Xab2	T	A	8: 3,666,094 (GRCm39)	D227V	probably damaging	Het
Zfp286	A	G	11: 62,674,534 (GRCm39)	S104P	possibly damaging	Het
Zfp345	T	C	2: 150,316,741 (GRCm39)	D22G	probably damaging	Het

Other mutations in Ptpn23

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00327:Ptpn23	APN	9	110,217,174 (GRCm39)	missense	probably benign	0.00
IGL01462:Ptpn23	APN	9	110,237,175 (GRCm39)	missense	probably benign	0.33
IGL01666:Ptpn23	APN	9	110,215,613 (GRCm39)	missense	possibly damaging	0.95
IGL01757:Ptpn23	APN	9	110,220,704 (GRCm39)	missense	probably damaging	1.00
IGL02402:Ptpn23	APN	9	110,222,781 (GRCm39)	missense	possibly damaging	0.81
IGL02891:Ptpn23	APN	9	110,217,088 (GRCm39)	nonsense	probably null
peony	UTSW	9	110,215,575 (GRCm39)	missense	probably damaging	0.97
FR4449:Ptpn23	UTSW	9	110,216,701 (GRCm39)	missense	probably benign	0.15
FR4548:Ptpn23	UTSW	9	110,216,701 (GRCm39)	missense	probably benign	0.15
FR4737:Ptpn23	UTSW	9	110,216,701 (GRCm39)	missense	probably benign	0.15
FR4976:Ptpn23	UTSW	9	110,216,701 (GRCm39)	missense	probably benign	0.15
R0111:Ptpn23	UTSW	9	110,214,691 (GRCm39)	missense	probably damaging	0.97
R0377:Ptpn23	UTSW	9	110,217,200 (GRCm39)	missense	possibly damaging	0.73
R0432:Ptpn23	UTSW	9	110,218,078 (GRCm39)	critical splice donor site	probably null
R0456:Ptpn23	UTSW	9	110,218,861 (GRCm39)	splice site	probably null
R0457:Ptpn23	UTSW	9	110,215,361 (GRCm39)	missense	possibly damaging	0.95
R0988:Ptpn23	UTSW	9	110,217,845 (GRCm39)	missense	probably benign	0.02
R1072:Ptpn23	UTSW	9	110,215,663 (GRCm39)	missense	probably benign	0.29
R1769:Ptpn23	UTSW	9	110,220,746 (GRCm39)	missense	possibly damaging	0.89
R1859:Ptpn23	UTSW	9	110,217,938 (GRCm39)	missense	possibly damaging	0.92
R1891:Ptpn23	UTSW	9	110,222,868 (GRCm39)	missense	possibly damaging	0.74
R1915:Ptpn23	UTSW	9	110,215,575 (GRCm39)	missense	probably damaging	0.97
R2299:Ptpn23	UTSW	9	110,221,581 (GRCm39)	missense	possibly damaging	0.72
R2431:Ptpn23	UTSW	9	110,215,347 (GRCm39)	nonsense	probably null
R2445:Ptpn23	UTSW	9	110,216,700 (GRCm39)	missense	possibly damaging	0.79
R3014:Ptpn23	UTSW	9	110,218,763 (GRCm39)	missense	probably benign
R3820:Ptpn23	UTSW	9	110,218,862 (GRCm39)	unclassified	probably benign
R3904:Ptpn23	UTSW	9	110,218,313 (GRCm39)	missense	probably benign	0.11
R4441:Ptpn23	UTSW	9	110,221,793 (GRCm39)	missense	probably benign	0.01
R4464:Ptpn23	UTSW	9	110,215,881 (GRCm39)	missense	probably damaging	1.00
R4709:Ptpn23	UTSW	9	110,217,924 (GRCm39)	missense	possibly damaging	0.86
R4810:Ptpn23	UTSW	9	110,218,204 (GRCm39)	missense	possibly damaging	0.93
R4937:Ptpn23	UTSW	9	110,221,806 (GRCm39)	missense	probably benign	0.09
R5023:Ptpn23	UTSW	9	110,217,624 (GRCm39)	missense	probably benign	0.00
R5057:Ptpn23	UTSW	9	110,217,624 (GRCm39)	missense	probably benign	0.00
R5065:Ptpn23	UTSW	9	110,227,256 (GRCm39)	missense	possibly damaging	0.91
R5143:Ptpn23	UTSW	9	110,214,506 (GRCm39)	unclassified	probably benign
R5370:Ptpn23	UTSW	9	110,214,769 (GRCm39)	missense	possibly damaging	0.79
R5534:Ptpn23	UTSW	9	110,221,809 (GRCm39)	missense	possibly damaging	0.95
R5715:Ptpn23	UTSW	9	110,216,143 (GRCm39)	missense	probably damaging	1.00
R5914:Ptpn23	UTSW	9	110,214,511 (GRCm39)	unclassified	probably benign
R6122:Ptpn23	UTSW	9	110,216,893 (GRCm39)	unclassified	probably benign
R6155:Ptpn23	UTSW	9	110,216,849 (GRCm39)	unclassified	probably benign
R6156:Ptpn23	UTSW	9	110,216,849 (GRCm39)	unclassified	probably benign
R6296:Ptpn23	UTSW	9	110,222,894 (GRCm39)	missense	probably damaging	0.96
R6755:Ptpn23	UTSW	9	110,218,855 (GRCm39)	missense	probably damaging	0.98
R7018:Ptpn23	UTSW	9	110,214,884 (GRCm39)	missense	possibly damaging	0.89
R7126:Ptpn23	UTSW	9	110,217,812 (GRCm39)	missense	probably benign	0.00
R7181:Ptpn23	UTSW	9	110,214,325 (GRCm39)	missense	unknown
R7578:Ptpn23	UTSW	9	110,216,676 (GRCm39)	missense	probably benign	0.33
R7675:Ptpn23	UTSW	9	110,216,094 (GRCm39)	nonsense	probably null
R7776:Ptpn23	UTSW	9	110,215,368 (GRCm39)	missense	possibly damaging	0.89
R7797:Ptpn23	UTSW	9	110,222,875 (GRCm39)	missense	possibly damaging	0.86
R8071:Ptpn23	UTSW	9	110,217,268 (GRCm39)	missense	possibly damaging	0.93
R8071:Ptpn23	UTSW	9	110,217,267 (GRCm39)	missense	probably damaging	0.98
R8954:Ptpn23	UTSW	9	110,221,568 (GRCm39)	missense	probably damaging	1.00
R9063:Ptpn23	UTSW	9	110,218,693 (GRCm39)	missense	possibly damaging	0.85
R9208:Ptpn23	UTSW	9	110,237,101 (GRCm39)	critical splice donor site	probably null
R9380:Ptpn23	UTSW	9	110,221,581 (GRCm39)	missense	possibly damaging	0.72
R9404:Ptpn23	UTSW	9	110,216,025 (GRCm39)	missense
R9570:Ptpn23	UTSW	9	110,227,217 (GRCm39)	missense	probably damaging	0.96
R9649:Ptpn23	UTSW	9	110,215,226 (GRCm39)	critical splice acceptor site	probably null
X0062:Ptpn23	UTSW	9	110,216,775 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- ATAGAGCAACGCGAAGGCTC -3'
(R):5'- TACTGAGACCCATGTGGAGC -3'

Sequencing Primer
(F):5'- AACGCGAAGGCTCCTGTG -3'
(R):5'- TCTGCAGTTCCGGGATCAGAG -3'

Posted On

2014-08-01