Mutagenetix > Incidental Mutation

Incidental Mutation 'R3974:Pcdhb4'

312558

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb4

Ensembl Gene

ENSMUSG00000045689

Gene Name

protocadherin beta 4

Synonyms

PcdhbD, Pcdhb5A

Accession Numbers

Ncbi RefSeq: NM_053129.3; MGI:2136738

Essential gene?

Probably non essential (E-score: 0.060) question?

Stock #

R3974 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

37307455-37311172 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37308848 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 404 (T404A)

Ref Sequence

ENSEMBL: ENSMUSP00000059770 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000051754] [ENSMUST00000056712] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91XZ6

Predicted Effect

probably benign
Transcript: ENSMUST00000051754

SMART Domains

Protein: ENSMUSP00000059180
Gene: ENSMUSG00000045498

Domain	Start	End	E-Value	Type
low complexity region	14	28	N/A	INTRINSIC
CA	44	131	6.29e-1	SMART
CA	155	240	7.16e-21	SMART
CA	264	345	1.22e-23	SMART
CA	368	449	2.86e-20	SMART
CA	473	559	2.55e-26	SMART
CA	589	670	1.11e-8	SMART
Pfam:Cadherin_C_2	687	770	9.9e-25	PFAM

Predicted Effect

possibly damaging
Transcript: ENSMUST00000056712
AA Change: T404A

PolyPhen 2 Score 0.551 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000059770
Gene: ENSMUSG00000045689
AA Change: T404A

Domain	Start	End	E-Value	Type
CA	54	131	1.66e0	SMART
CA	155	240	1.07e-19	SMART
CA	264	344	6.03e-28	SMART
CA	367	448	2.57e-22	SMART
CA	472	558	3.36e-26	SMART
CA	588	669	3.48e-10	SMART
Pfam:Cadherin_C_2	685	768	1e-25	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115661

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458

Domain	Start	End	E-Value	Type
CA	20	131	5.3e-2	SMART
CA	155	240	1.51e-19	SMART
CA	264	348	7.6e-25	SMART
CA	372	453	1.42e-24	SMART
CA	477	563	1.42e-24	SMART
CA	594	674	4.12e-12	SMART
low complexity region	706	721	N/A	INTRINSIC
Pfam:Cadherin_tail	796	930	3.9e-58	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000193025

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000194544

SMART Domains

Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

Domain	Start	End	E-Value	Type
Blast:CA	18	66	5e-20	BLAST

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.9%
20x: 93.8%

Validation Efficiency

Allele List at MGI

Other mutations in this stock

Total: 53 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510039O18Rik	T	C	4: 147,945,031	I486T	probably damaging	Het
Abca8a	A	T	11: 110,083,502	M202K	probably damaging	Het
Abhd4	T	A	14: 54,262,960	I117N	probably damaging	Het
Adam23	T	A	1: 63,547,729	Y416*	probably null	Het
Cenpe	A	G	3: 135,235,225		probably null	Het
Cenph	A	G	13: 100,763,567	V151A	probably damaging	Het
Cfap54	A	G	10: 92,839,471	S2863P	possibly damaging	Het
Clca1	A	T	3: 145,032,639	V36D	probably damaging	Het
Cnbd1	G	A	4: 18,887,693	R274C	probably benign	Het
Crot	T	C	5: 8,977,541	T264A	probably benign	Het
Dll4	A	G	2: 119,334,092	D664G	probably damaging	Het
Ehbp1	C	T	11: 22,137,867	A406T	probably benign	Het
Far2	T	A	6: 148,150,754	I177N	probably damaging	Het
Flt4	T	G	11: 49,636,740	V910G	probably damaging	Het
Fmod	A	G	1: 134,040,758	R179G	probably benign	Het
Gdf2	T	A	14: 33,944,834	V171D	probably damaging	Het
Gm884	A	T	11: 103,619,101		probably benign	Het
Gpx6	C	A	13: 21,317,658	S150Y	probably damaging	Het
Grik2	A	T	10: 49,422,654	Y37N	probably damaging	Het
Grn	T	C	11: 102,436,339	V559A	probably damaging	Het
Muc2	T	A	7: 141,746,804		probably benign	Het
Myo5b	T	C	18: 74,634,481	Y287H	probably damaging	Het
Nbeal2	T	C	9: 110,633,846	T1350A	probably damaging	Het
Nfkbiz	T	C	16: 55,818,436	I220M	probably benign	Het
Nt5dc2	T	C	14: 31,138,875	S439P	probably damaging	Het
Olfr1049	A	T	2: 86,255,591	I34N	possibly damaging	Het
Olfr598	T	G	7: 103,329,078	D197E	probably damaging	Het
Omg	T	A	11: 79,502,398	E211D	probably benign	Het
Plcl1	T	A	1: 55,698,215	M905K	probably benign	Het
Plod2	G	T	9: 92,598,619	G422*	probably null	Het
Ppp1r12a	T	C	10: 108,253,480	V660A	probably benign	Het
Prdm6	T	C	18: 53,540,206	I186T	possibly damaging	Het
Ptprq	T	G	10: 107,712,062	K158N	possibly damaging	Het
Rimbp2	A	G	5: 128,797,798	V243A	probably damaging	Het
Rp1l1	T	A	14: 64,030,309	Y1115N	probably damaging	Het
Rtn4	C	T	11: 29,707,505	T553I	probably damaging	Het
Scrn3	T	C	2: 73,335,777	S385P	possibly damaging	Het
Serpina1f	C	A	12: 103,693,571	G151*	probably null	Het
Sis	T	C	3: 72,943,635	T577A	probably damaging	Het
Slco1a1	A	T	6: 141,909,093	S611T	probably benign	Het
Smad4	G	T	18: 73,677,736	T59K	possibly damaging	Het
Syne1	T	C	10: 5,043,630	D8370G	probably benign	Het
Tigd4	G	A	3: 84,595,278	A501T	possibly damaging	Het
Tjp1	A	T	7: 65,297,639	C1724*	probably null	Het
Tmem107	G	T	11: 69,071,475		probably null	Het
Tsc22d1	T	C	14: 76,418,609	S761P	probably damaging	Het
Tyw5	A	T	1: 57,391,528	D165E	probably damaging	Het
U2af2	T	A	7: 5,069,439		probably null	Het
Ube3b	T	A	5: 114,412,430	D839E	probably benign	Het
Ush2a	A	G	1: 188,381,501	D639G	probably benign	Het
Veph1	A	T	3: 66,158,227	M473K	probably benign	Het
Vmn2r72	A	T	7: 85,749,809	N445K	probably damaging	Het
Vps37d	T	C	5: 135,076,539	M77V	probably null	Het

Other mutations in Pcdhb4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00490:Pcdhb4	APN	18	37309916	missense	possibly damaging	0.68
IGL01319:Pcdhb4	APN	18	37308513	missense	probably benign
IGL01325:Pcdhb4	APN	18	37309623	missense	probably damaging	1.00
IGL01608:Pcdhb4	APN	18	37308750	missense	probably damaging	1.00
IGL01808:Pcdhb4	APN	18	37309014	missense	probably damaging	1.00
IGL01962:Pcdhb4	APN	18	37309004	missense	possibly damaging	0.90
IGL02280:Pcdhb4	APN	18	37307682	missense	probably benign	0.00
IGL02622:Pcdhb4	APN	18	37309668	missense	probably benign	0.00
IGL03025:Pcdhb4	APN	18	37309977	missense	possibly damaging	0.62
IGL03137:Pcdhb4	APN	18	37308516	missense	probably damaging	0.98
P0031:Pcdhb4	UTSW	18	37308885	missense	probably damaging	1.00
R0385:Pcdhb4	UTSW	18	37309215	missense	probably damaging	1.00
R0611:Pcdhb4	UTSW	18	37308210	missense	probably damaging	1.00
R0671:Pcdhb4	UTSW	18	37307742	missense	probably benign	0.01
R0738:Pcdhb4	UTSW	18	37308711	missense	probably damaging	1.00
R0853:Pcdhb4	UTSW	18	37309885	nonsense	probably null
R0893:Pcdhb4	UTSW	18	37309370	splice site	probably null
R1932:Pcdhb4	UTSW	18	37309541	missense	probably benign	0.33
R1945:Pcdhb4	UTSW	18	37308868	missense	probably damaging	1.00
R2194:Pcdhb4	UTSW	18	37308735	missense	probably damaging	1.00
R2273:Pcdhb4	UTSW	18	37308926	missense	probably damaging	1.00
R3807:Pcdhb4	UTSW	18	37309314	missense	probably damaging	0.98
R3815:Pcdhb4	UTSW	18	37308012	missense	probably damaging	1.00
R3816:Pcdhb4	UTSW	18	37308012	missense	probably damaging	1.00
R4558:Pcdhb4	UTSW	18	37309964	missense	probably benign
R4606:Pcdhb4	UTSW	18	37308652	missense	probably damaging	1.00
R4615:Pcdhb4	UTSW	18	37308500	missense	probably benign	0.02
R4840:Pcdhb4	UTSW	18	37308399	missense	possibly damaging	0.60
R5240:Pcdhb4	UTSW	18	37309926	missense	possibly damaging	0.78
R5272:Pcdhb4	UTSW	18	37307766	missense	probably benign	0.04
R5586:Pcdhb4	UTSW	18	37308981	missense	probably damaging	1.00
R5683:Pcdhb4	UTSW	18	37308989	missense	probably benign	0.45
R5917:Pcdhb4	UTSW	18	37309566	missense	probably damaging	1.00
R6110:Pcdhb4	UTSW	18	37308429	missense	possibly damaging	0.80
R6383:Pcdhb4	UTSW	18	37308021	missense	probably damaging	1.00
R6877:Pcdhb4	UTSW	18	37309572	missense	probably damaging	1.00
R7036:Pcdhb4	UTSW	18	37308782	missense	possibly damaging	0.95
R7204:Pcdhb4	UTSW	18	37309239	missense	probably damaging	1.00
R7271:Pcdhb4	UTSW	18	37308169	missense	possibly damaging	0.89
R7436:Pcdhb4	UTSW	18	37309275	missense	probably damaging	1.00
R7444:Pcdhb4	UTSW	18	37309452	missense	probably damaging	1.00
R7614:Pcdhb4	UTSW	18	37309549	missense	probably benign	0.40
R7650:Pcdhb4	UTSW	18	37309614	missense	probably damaging	1.00
R7664:Pcdhb4	UTSW	18	37309240	missense	probably damaging	1.00
R8080:Pcdhb4	UTSW	18	37309296	missense	probably benign	0.42
R8087:Pcdhb4	UTSW	18	37308664	missense	probably damaging	1.00
R8115:Pcdhb4	UTSW	18	37309400	missense	probably damaging	0.99
R8697:Pcdhb4	UTSW	18	37308779	missense	probably benign	0.15
R8815:Pcdhb4	UTSW	18	37309002	missense	probably damaging	1.00
R9008:Pcdhb4	UTSW	18	37307661	missense	probably benign
R9225:Pcdhb4	UTSW	18	37308642	missense	possibly damaging	0.68
R9278:Pcdhb4	UTSW	18	37308872	missense	possibly damaging	0.61
R9299:Pcdhb4	UTSW	18	37309211	missense	probably benign	0.02
R9390:Pcdhb4	UTSW	18	37309728	missense	possibly damaging	0.80
R9582:Pcdhb4	UTSW	18	37308364	missense	probably damaging	1.00
R9686:Pcdhb4	UTSW	18	37309890	missense	probably damaging	0.98
R9721:Pcdhb4	UTSW	18	37309852	missense	possibly damaging	0.70
Z1177:Pcdhb4	UTSW	18	37309913	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- ATGATAACGCCCCAGAGTTGAC -3'
(R):5'- CTGATGGTGCCTATGTGCAG -3'

Sequencing Primer
(F):5'- AGAGTTGACGGTCTCTACGCTC -3'
(R):5'- CTGTTGTTCTCATGGACAAACAGG -3'

Posted On

2015-04-30