Mutagenetix > Incidental Mutation

Incidental Mutation 'R4223:Ptbp1'

319467

Institutional Source

Beutler Lab

Gene Symbol

Ptbp1

Ensembl Gene

ENSMUSG00000006498

Gene Name

polypyrimidine tract binding protein 1

Synonyms

Ptb, hnRNP I

MMRRC Submission

041043-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R4223 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

79690502-79700269 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 79695047 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Threonine at position 125 (I125T)

Ref Sequence

ENSEMBL: ENSMUSP00000059481 (fasta)

Gene Model

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

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000057343
AA Change: I125T

PolyPhen 2 Score 0.070 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000059481
Gene: ENSMUSG00000006498
AA Change: I125T

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 benign
Transcript: ENSMUST00000095457
AA Change: I85T

PolyPhen 2 Score 0.062 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000093109
Gene: ENSMUSG00000006498
AA Change: I85T

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: I125T

PolyPhen 2 Score 0.035 (Sensitivity: 0.94; Specificity: 0.82)

SMART Domains

Protein: ENSMUSP00000127783
Gene: ENSMUSG00000006498
AA Change: I125T

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

SMART Domains

Protein: ENSMUSP00000130749
Gene: ENSMUSG00000006498

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

noncoding transcript
Transcript: ENSMUST00000171216

Predicted Effect

probably benign
Transcript: ENSMUST00000172282
AA Change: I125T

PolyPhen 2 Score 0.009 (Sensitivity: 0.96; Specificity: 0.77)

SMART Domains

Protein: ENSMUSP00000126192
Gene: ENSMUSG00000006498
AA Change: I125T

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: ENSMUST00000168988

Predicted Effect

unknown
Transcript: ENSMUST00000169091
AA Change: I75T

SMART Domains

Protein: ENSMUSP00000128449
Gene: ENSMUSG00000006498
AA Change: I75T

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

noncoding transcript
Transcript: ENSMUST00000184090

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168521

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000168216

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000166593

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000169580

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: 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

noncoding transcript
Transcript: ENSMUST00000217802

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

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

Meta Mutation Damage Score

0.3424

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.6%

Validation Efficiency

98% (65/66)

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
2610008E11Rik	A	G	10: 78,930,286 (GRCm39)	Y43H	probably damaging	Het
Aamp	A	T	1: 74,320,285 (GRCm39)	L348Q	probably damaging	Het
Abcb1b	T	A	5: 8,863,722 (GRCm39)	L226M	probably damaging	Het
Acap1	A	G	11: 69,774,511 (GRCm39)	S396P	probably damaging	Het
Aif1l	A	T	2: 31,852,251 (GRCm39)	S40C	probably damaging	Het
Atp1a3	T	C	7: 24,700,355 (GRCm39)	D48G	probably benign	Het
Bhmt-ps1	T	A	4: 26,369,352 (GRCm39)		noncoding transcript	Het
Ccdc116	A	G	16: 16,964,809 (GRCm39)		probably benign	Het
Cmtm5	T	A	14: 55,175,376 (GRCm39)	C51S	probably damaging	Het
Cyb5rl	T	C	4: 106,938,185 (GRCm39)	V214A	probably damaging	Het
Cyp4x1	A	T	4: 114,970,077 (GRCm39)	I350N	probably damaging	Het
Efcab6	C	A	15: 83,751,309 (GRCm39)	D1498Y	probably damaging	Het
Eif3c	C	G	7: 126,165,471 (GRCm39)		probably benign	Het
Epha3	G	A	16: 63,403,902 (GRCm39)	S733L	probably damaging	Het
Esyt1	T	C	10: 128,356,517 (GRCm39)	Y376C	probably damaging	Het
Galnt1	T	C	18: 24,371,413 (GRCm39)	F4L	probably benign	Het
Glis1	T	C	4: 107,425,042 (GRCm39)	S218P	probably benign	Het
Gm15854	A	T	6: 129,949,426 (GRCm39)		noncoding transcript	Het
Gm29125	T	C	1: 80,361,236 (GRCm39)		noncoding transcript	Het
Inpp5a	T	C	7: 139,138,821 (GRCm39)	V263A	possibly damaging	Het
Itgb1	T	G	8: 129,440,624 (GRCm39)	I255S	probably damaging	Het
Kcp	A	G	6: 29,482,257 (GRCm39)	L1547P	possibly damaging	Het
Kifc3	C	A	8: 95,836,610 (GRCm39)	L72F	probably damaging	Het
Lama3	T	C	18: 12,583,460 (GRCm39)	C683R	probably damaging	Het
Lrrc55	G	A	2: 85,026,460 (GRCm39)	A188V	possibly damaging	Het
Ly6i	A	T	15: 74,854,884 (GRCm39)	S9T	probably benign	Het
Mfsd14b	C	T	13: 65,214,422 (GRCm39)		probably benign	Het
Nipsnap3a	T	A	4: 52,997,251 (GRCm39)	D172E	probably benign	Het
Or4g7	A	T	2: 111,309,489 (GRCm39)	Y120F	probably benign	Het
Oxgr1	T	C	14: 120,260,025 (GRCm39)	K61E	probably damaging	Het
Pak2	G	T	16: 31,871,028 (GRCm39)	N51K	probably benign	Het
Pcdhgb7	T	A	18: 37,886,856 (GRCm39)	D675E	probably benign	Het
Pcolce	T	A	5: 137,603,389 (GRCm39)		probably benign	Het
Phc3	A	T	3: 30,990,968 (GRCm39)	S383R	probably damaging	Het
Phf1	C	T	17: 27,156,474 (GRCm39)	R539*	probably null	Het
Plch1	G	A	3: 63,609,321 (GRCm39)	T48I	probably damaging	Het
Plekha2	A	G	8: 25,533,036 (GRCm39)	S312P	probably damaging	Het
Pnpla7	T	C	2: 24,872,126 (GRCm39)	F69L	possibly damaging	Het
Ppcdc	T	A	9: 57,321,998 (GRCm39)	M181L	possibly damaging	Het
Rfc3	C	A	5: 151,574,637 (GRCm39)		probably benign	Het
Rpa2	T	G	4: 132,504,055 (GRCm39)	I69S	probably damaging	Het
Rtn4	G	A	11: 29,656,856 (GRCm39)	V337I	probably benign	Het
Rttn	T	C	18: 89,113,708 (GRCm39)	L1709P	probably damaging	Het
Sh2b2	G	A	5: 136,247,907 (GRCm39)	P548L	possibly damaging	Het
Slc12a2	T	A	18: 58,043,328 (GRCm39)	S591T	probably damaging	Het
Slc25a45	A	T	19: 5,930,146 (GRCm39)	I39F	probably damaging	Het
Slc38a9	G	A	13: 112,850,782 (GRCm39)		probably null	Het
Slc9a4	T	C	1: 40,658,286 (GRCm39)	V603A	probably damaging	Het
Snx19	T	G	9: 30,339,744 (GRCm39)	V294G	possibly damaging	Het
Sp140l2	T	C	1: 85,090,278 (GRCm39)	D83G	probably damaging	Het
Sspo	G	T	6: 48,428,091 (GRCm39)	V313L	possibly damaging	Het
Stard9	A	G	2: 120,495,472 (GRCm39)	T116A	possibly damaging	Het
Strn3	C	T	12: 51,674,638 (GRCm39)	R382Q	probably damaging	Het
Trim43b	T	A	9: 88,972,692 (GRCm39)	Q154L	probably benign	Het
Trps1	A	G	15: 50,710,044 (GRCm39)	V98A	probably benign	Het
Vmn1r220	T	A	13: 23,368,148 (GRCm39)	M183L	probably benign	Het
Vmn2r60	A	T	7: 41,765,952 (GRCm39)	T20S	probably benign	Het
Wdr81	T	C	11: 75,338,828 (GRCm39)	T1444A	probably benign	Het
Xirp2	A	T	2: 67,346,837 (GRCm39)	E3026V	possibly 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
R2418:Ptbp1	UTSW	10	79,695,511 (GRCm39)	missense	probably damaging	0.98
R4222: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'- TTCCAGAGTCATCCATGTCAG -3'
(R):5'- AAGGCCAGGTTTCCAGACTG -3'

Sequencing Primer
(F):5'- GAGTCATCCATGTCAGAAAGCTGC -3'
(R):5'- ACTGGACGGAGTTTACAG -3'

Posted On

2015-06-10