Mutagenetix > Incidental Mutation

Incidental Mutation 'R2418:Ptbp1'

249084

Institutional Source

Beutler Lab

Gene Symbol

Ptbp1

Ensembl Gene

ENSMUSG00000006498

Gene Name

polypyrimidine tract binding protein 1

Synonyms

Ptb, hnRNP I

MMRRC Submission

040380-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R2418 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

79690502-79700269 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 79695511 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 187 (Y187H)

Ref Sequence

ENSEMBL: ENSMUSP00000093109 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000057343] [ENSMUST00000095457] [ENSMUST00000165704] [ENSMUST00000165724] [ENSMUST00000172282] [ENSMUST00000168683] [ENSMUST00000167250] [ENSMUST00000169483] [ENSMUST00000171599]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000057343
AA Change: Y227H

PolyPhen 2 Score 0.044 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000059481
Gene: ENSMUSG00000006498
AA Change: Y227H

Domain	Start	End	E-Value	Type
low complexity region	32	38	N/A	INTRINSIC
RRM	59	128	9.8e-9	SMART
low complexity region	161	178	N/A	INTRINSIC
RRM	184	253	4.75e-7	SMART
low complexity region	305	330	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000095457
AA Change: Y187H

PolyPhen 2 Score 0.982 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000093109
Gene: ENSMUSG00000006498
AA Change: Y187H

Domain	Start	End	E-Value	Type
Pfam:RRM_6	36	86	1.9e-5	PFAM
Pfam:RRM_5	38	90	3.6e-12	PFAM
low complexity region	121	138	N/A	INTRINSIC
RRM	144	213	4.75e-7	SMART
low complexity region	265	290	N/A	INTRINSIC
RRM	296	365	1.84e-13	SMART
RRM	413	483	2.6e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000099958

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000164385

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000165153

Predicted Effect

probably benign
Transcript: ENSMUST00000165704
AA Change: Y227H

PolyPhen 2 Score 0.179 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000127783
Gene: ENSMUSG00000006498
AA Change: Y227H

Domain	Start	End	E-Value	Type
low complexity region	32	38	N/A	INTRINSIC
RRM	59	128	9.8e-9	SMART
low complexity region	161	178	N/A	INTRINSIC
RRM	184	253	4.75e-7	SMART
low complexity region	305	330	N/A	INTRINSIC
RRM	336	405	1.84e-13	SMART
RRM	453	523	2.6e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000165724
AA Change: Y10H

PolyPhen 2 Score 0.365 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000130749
Gene: ENSMUSG00000006498
AA Change: Y10H

Domain	Start	End	E-Value	Type
Pfam:RRM_5	2	40	5.3e-7	PFAM
low complexity region	114	139	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000172282
AA Change: Y227H

PolyPhen 2 Score 0.173 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000126192
Gene: ENSMUSG00000006498
AA Change: Y227H

Domain	Start	End	E-Value	Type
low complexity region	32	38	N/A	INTRINSIC
RRM	59	128	9.8e-9	SMART
low complexity region	161	178	N/A	INTRINSIC
RRM	184	253	4.75e-7	SMART
low complexity region	331	356	N/A	INTRINSIC
RRM	362	431	1.84e-13	SMART
RRM	479	549	2.6e-13	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168521

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169580

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000171216

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168988

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166593

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000184090

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168216

Predicted Effect

probably benign
Transcript: ENSMUST00000169091

SMART Domains

Protein: ENSMUSP00000128449
Gene: ENSMUSG00000006498

Domain	Start	End	E-Value	Type
low complexity region	13	19	N/A	INTRINSIC
Pfam:RRM_5	29	81	3.5e-12	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000168683

SMART Domains

Protein: ENSMUSP00000132383
Gene: ENSMUSG00000006498

Domain	Start	End	E-Value	Type
low complexity region	2	8	N/A	INTRINSIC
SCOP:d2u1a__	17	55	3e-3	SMART
PDB:2AD9\|A	18	55	9e-19	PDB
Blast:RRM	29	55	2e-11	BLAST

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000217802

Predicted Effect

probably benign
Transcript: ENSMUST00000167250

SMART Domains

Protein: ENSMUSP00000130695
Gene: ENSMUSG00000035835

Domain	Start	End	E-Value	Type
transmembrane domain	17	39	N/A	INTRINSIC
transmembrane domain	69	91	N/A	INTRINSIC
acidPPc	132	276	1.38e-16	SMART
low complexity region	437	454	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000169483

SMART Domains

Protein: ENSMUSP00000127507
Gene: ENSMUSG00000006498

Domain	Start	End	E-Value	Type
low complexity region	32	38	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000171599

SMART Domains

Protein: ENSMUSP00000131296
Gene: ENSMUSG00000006498

Domain	Start	End	E-Value	Type
low complexity region	87	93	N/A	INTRINSIC

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.8%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the subfamily of ubiquitously expressed heterogeneous nuclear ribonucleoproteins (hnRNPs). The hnRNPs are RNA-binding proteins and they complex with heterogeneous nuclear RNA (hnRNA). These proteins are associated with pre-mRNAs in the nucleus and appear to influence pre-mRNA processing and other aspects of mRNA metabolism and transport. While all of the hnRNPs are present in the nucleus, some seem to shuttle between the nucleus and the cytoplasm. The hnRNP proteins have distinct nucleic acid binding properties. The protein encoded by this gene has four repeats of quasi-RNA recognition motif (RRM) domains that bind RNAs. This protein binds to the intronic polypyrimidine tracts that requires pre-mRNA splicing and acts via the protein degradation ubiquitin-proteasome pathway. It may also promote the binding of U2 snRNP to pre-mRNAs. This protein is localized in the nucleoplasm and it is also detected in the perinucleolar structure. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele die before E6.5. Mice homozygous for a conditional allele activated in neuronal stem cells (NSCs) exhibit premature death, and non-obstructive hydrocephaly with loss of ependymal cells due to precocious NSC differentiation. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca2	G	A	2: 25,328,001 (GRCm39)	A768T	probably benign	Het
Acox3	A	G	5: 35,761,982 (GRCm39)	N442S	probably benign	Het
Acp5	C	A	9: 22,041,248 (GRCm39)	V60L	probably benign	Het
Arap3	T	C	18: 38,122,997 (GRCm39)	D501G	probably damaging	Het
Bcorl1	A	G	X: 47,459,418 (GRCm39)	T425A	probably damaging	Het
Btd	G	A	14: 31,363,093 (GRCm39)		probably null	Het
Cfap251	A	C	5: 123,392,331 (GRCm39)		probably benign	Het
Cfap74	T	A	4: 155,540,166 (GRCm39)		probably benign	Het
Cnot8	G	A	11: 58,006,136 (GRCm39)	G222R	probably damaging	Het
Col4a4	G	T	1: 82,510,657 (GRCm39)	A205E	unknown	Het
Cwf19l1	T	C	19: 44,119,911 (GRCm39)	T77A	probably benign	Het
Cyp2b9	A	G	7: 25,886,132 (GRCm39)	T100A	probably benign	Het
Ddx24	A	G	12: 103,383,996 (GRCm39)	L485P	probably damaging	Het
Dnah9	A	T	11: 65,986,241 (GRCm39)	L1131*	probably null	Het
Dnase1l3	T	A	14: 7,968,089 (GRCm38)	E272V	possibly damaging	Het
Dscc1	G	A	15: 54,946,820 (GRCm39)	R302*	probably null	Het
Elk3	T	C	10: 93,120,689 (GRCm39)	N50S	probably damaging	Het
Fmo3	A	T	1: 162,794,527 (GRCm39)	I181K	probably benign	Het
Golga3	T	C	5: 110,349,734 (GRCm39)	I655T	probably damaging	Het
Hspa1l	A	T	17: 35,196,164 (GRCm39)	T68S	probably benign	Het
Itgax	C	T	7: 127,741,505 (GRCm39)	R839W	probably damaging	Het
Itk	A	G	11: 46,229,044 (GRCm39)	F379L	probably damaging	Het
Kif7	C	A	7: 79,348,441 (GRCm39)	R1300L	probably benign	Het
Klkb1	A	T	8: 45,742,149 (GRCm39)	D43E	possibly damaging	Het
Kmt5b	C	T	19: 3,857,266 (GRCm39)	A318V	probably benign	Het
Krt78	T	C	15: 101,855,069 (GRCm39)	Y914C	probably benign	Het
Lactb2	T	C	1: 13,730,563 (GRCm39)	T38A	possibly damaging	Het
Lmbr1l	A	C	15: 98,805,418 (GRCm39)	F361C	possibly damaging	Het
Magi1	T	C	6: 93,722,891 (GRCm39)	D329G	probably damaging	Het
Map3k5	T	A	10: 19,986,603 (GRCm39)	V939E	probably benign	Het
Mcm8	C	T	2: 132,666,658 (GRCm39)	A233V	probably benign	Het
Mcur1	C	T	13: 43,703,013 (GRCm39)	V241M	possibly damaging	Het
Mical2	G	T	7: 111,919,941 (GRCm39)		probably null	Het
Nudt13	A	G	14: 20,361,581 (GRCm39)	E219G	probably damaging	Het
Or4c107	A	G	2: 88,789,380 (GRCm39)	N190S	probably benign	Het
Or52d3	A	T	7: 104,229,141 (GRCm39)	H96L	probably benign	Het
Or6b1	A	G	6: 42,814,983 (GRCm39)	H56R	probably benign	Het
Osbpl7	A	C	11: 96,950,004 (GRCm39)	D395A	probably benign	Het
Osbpl9	A	G	4: 108,923,415 (GRCm39)	C495R	probably damaging	Het
Pcdhac1	T	C	18: 37,224,381 (GRCm39)	L398P	probably benign	Het
Pcnx4	T	A	12: 72,603,037 (GRCm39)	F433Y	probably damaging	Het
Pdp1	G	A	4: 11,961,838 (GRCm39)	P158S	probably damaging	Het
Pkd1l3	A	C	8: 110,397,353 (GRCm39)	*2152C	probably null	Het
Plcxd3	G	T	15: 4,604,245 (GRCm39)	K284N	probably benign	Het
Plxnb2	A	G	15: 89,045,272 (GRCm39)	V1058A	possibly damaging	Het
Resp18	T	C	1: 75,248,955 (GRCm39)	*176W	probably null	Het
Rps6ka2	A	C	17: 7,566,738 (GRCm39)	Q665H	possibly damaging	Het
Rtn1	T	C	12: 72,351,052 (GRCm39)	T386A	probably benign	Het
Samt2	A	T	X: 153,358,223 (GRCm39)		probably null	Het
Scn1a	T	C	2: 66,104,187 (GRCm39)	N1663S	probably damaging	Het
Smyd1	A	T	6: 71,216,537 (GRCm39)	I70N	probably damaging	Het
Tas2r105	T	C	6: 131,664,410 (GRCm39)	E6G	probably damaging	Het
Tchh	G	T	3: 93,352,936 (GRCm39)	R792L	unknown	Het
Tenm3	C	T	8: 48,729,693 (GRCm39)	D1438N	possibly damaging	Het
Tmem184b	A	G	15: 79,250,143 (GRCm39)	Y211H	possibly damaging	Het
Top3a	C	A	11: 60,638,842 (GRCm39)	G551V	possibly damaging	Het
Vmn1r168	A	T	7: 23,240,824 (GRCm39)	N227I	probably benign	Het
Vmn1r203	T	A	13: 22,709,004 (GRCm39)	S262T	possibly damaging	Het
Vmn1r204	T	G	13: 22,740,420 (GRCm39)	L17R	probably damaging	Het

Other mutations in Ptbp1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01115:Ptbp1	APN	10	79,695,796 (GRCm39)	splice site	probably benign
IGL01335:Ptbp1	APN	10	79,698,708 (GRCm39)	splice site	probably null
IGL03119:Ptbp1	APN	10	79,695,458 (GRCm39)	missense	probably damaging	1.00
carillon	UTSW	10	79,694,897 (GRCm39)	missense	probably damaging	0.98
Citi	UTSW	10	79,695,766 (GRCm39)	missense	probably benign	0.31
R1433:Ptbp1	UTSW	10	79,699,107 (GRCm39)	missense	probably damaging	1.00
R4222:Ptbp1	UTSW	10	79,695,047 (GRCm39)	missense	probably benign	0.07
R4223:Ptbp1	UTSW	10	79,695,047 (GRCm39)	missense	probably benign	0.07
R4224:Ptbp1	UTSW	10	79,695,047 (GRCm39)	missense	probably benign	0.07
R4688:Ptbp1	UTSW	10	79,692,342 (GRCm39)	missense	possibly damaging	0.87
R5841:Ptbp1	UTSW	10	79,695,766 (GRCm39)	missense	probably benign	0.31
R6961:Ptbp1	UTSW	10	79,695,111 (GRCm39)	splice site	probably null
R7242:Ptbp1	UTSW	10	79,692,222 (GRCm39)	missense	unknown
R7579:Ptbp1	UTSW	10	79,694,954 (GRCm39)	missense	probably benign	0.02
R8341:Ptbp1	UTSW	10	79,699,045 (GRCm39)	missense	probably benign
R8832:Ptbp1	UTSW	10	79,699,023 (GRCm39)	missense	probably damaging	1.00
R9141:Ptbp1	UTSW	10	79,694,897 (GRCm39)	missense	probably damaging	0.98
R9426:Ptbp1	UTSW	10	79,694,897 (GRCm39)	missense	probably damaging	0.98
R9465:Ptbp1	UTSW	10	79,695,615 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- CCCAGTGCTCAGGATCATTGTG -3'
(R):5'- GACATTGAGACTGGTGAGCTTG -3'

Sequencing Primer
(F):5'- TGCTCAGGATCATTGTGGAAAACC -3'
(R):5'- CTTGGAGAAGTCGATGCGC -3'

Posted On

2014-11-12