Mutagenetix > Incidental Mutations

Incidental Mutation 'R0179:Pcdhb5'

23079

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb5

Ensembl Gene

ENSMUSG00000063687

Gene Name

protocadherin beta 5

Synonyms

Pcdhb4A, PcdhbE

MMRRC Submission

038447-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.099) question?

Stock #

R0179 (G1)

Quality Score

225

Status

Validated (trace)

Chromosome

Chromosomal Location

37320381-37323915 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 37322559 bp

Zygosity

Heterozygous

Amino Acid Change

Glycine to Aspartic acid at position 664 (G664D)

Ref Sequence

ENSEMBL: ENSMUSP00000077389 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000078271] [ENSMUST00000115661] [ENSMUST00000194544]

Predicted Effect

probably damaging
Transcript: ENSMUST00000078271
AA Change: G664D

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000077389
Gene: ENSMUSG00000063687
AA Change: G664D

Domain	Start	End	E-Value	Type
signal peptide	1	27	N/A	INTRINSIC
CA	46	130	1.55e0	SMART
CA	154	239	2.42e-18	SMART
CA	263	344	1.27e-26	SMART
CA	367	448	1.14e-23	SMART
CA	472	558	2.38e-26	SMART
CA	588	669	7.06e-11	SMART
Pfam:Cadherin_C_2	686	769	3.1e-26	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

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

Meta Mutation Damage Score

0.2665

Coding Region Coverage

1x: 99.1%
3x: 98.4%
10x: 96.8%
20x: 94.1%

Validation Efficiency

98% (81/83)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the protocadherin beta gene cluster, one of three related gene clusters tandemly linked on chromosome five. The gene clusters demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The beta cluster contains 16 genes and 3 pseudogenes, each encoding 6 extracellular cadherin domains and a cytoplasmic tail that deviates from others in the cadherin superfamily. The extracellular domains interact in a homophilic manner to specify differential cell-cell connections. Unlike the alpha and gamma clusters, the transcripts from these genes are made up of only one large exon, not sharing common 3' exons as expected. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins. Their specific functions are unknown but they most likely play a critical role in the establishment and function of specific cell-cell neural connections. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700022I11Rik	T	C	4: 42,972,214	S516P	probably benign	Het
4932431P20Rik	A	G	7: 29,535,940		noncoding transcript	Het
Adamts1	C	T	16: 85,795,465	S948N	probably benign	Het
Adck1	A	T	12: 88,459,172	M457L	possibly damaging	Het
Adprm	A	T	11: 67,038,225	H313Q	possibly damaging	Het
Adssl1	T	C	12: 112,632,269	I104T	probably benign	Het
Agxt2	A	C	15: 10,399,048	Q435P	possibly damaging	Het
Amotl1	G	A	9: 14,548,773	A890V	probably benign	Het
Ankrd50	A	G	3: 38,455,314	V968A	possibly damaging	Het
Brf2	T	C	8: 27,125,868	D163G	possibly damaging	Het
Cd226	C	A	18: 89,207,139	N53K	probably benign	Het
Cdc42ep2	T	C	19: 5,918,608	D23G	probably benign	Het
Cdc7	T	C	5: 106,965,039	S8P	probably benign	Het
Cdh8	C	T	8: 99,111,712	E499K	possibly damaging	Het
Chd7	T	A	4: 8,862,516	F2534L	probably benign	Het
Ckb	T	C	12: 111,670,176	T255A	probably benign	Het
Cntnap5c	G	T	17: 57,769,625	W19L	probably benign	Het
Cntrl	A	G	2: 35,167,859	E1854G	probably benign	Het
Colec12	C	T	18: 9,858,921	P568L	unknown	Het
Cop1	A	G	1: 159,250,066	D157G	probably benign	Het
Csf2rb	A	C	15: 78,336,372	Q38P	possibly damaging	Het
Ctla2b	T	C	13: 60,896,293	D52G	possibly damaging	Het
Dcaf7	A	T	11: 106,051,797	D190V	probably damaging	Het
Depdc5	T	A	5: 32,901,574		probably benign	Het
Dgkq	A	G	5: 108,658,200		probably benign	Het
Dhrs2	A	G	14: 55,240,476	T222A	probably damaging	Het
Dock1	G	A	7: 135,098,837	D1109N	probably damaging	Het
E4f1	G	C	17: 24,451,437	T92S	possibly damaging	Het
Ep400	A	T	5: 110,668,649	S2669T	probably damaging	Het
Eprs	T	G	1: 185,413,547	D1184E	probably benign	Het
Fpr-rs4	A	T	17: 18,022,027	K99*	probably null	Het
Fzr1	A	T	10: 81,369,070		probably benign	Het
Gcc2	C	T	10: 58,276,650	R1001C	probably benign	Het
Gm4884	A	G	7: 41,043,828	D407G	probably benign	Het
Golga4	A	T	9: 118,560,740		probably null	Het
Gp2	T	G	7: 119,452,317	D225A	possibly damaging	Het
Gramd1a	T	A	7: 31,142,418	T120S	probably damaging	Het
Hbb-bh2	T	A	7: 103,839,227	N121I	probably benign	Het
Htr6	A	T	4: 139,062,126	L276Q	probably damaging	Het
Itga9	A	T	9: 118,661,386	I262F	probably benign	Het
Lamc3	A	G	2: 31,915,084		probably benign	Het
Large1	T	C	8: 73,098,846	N200S	probably benign	Het
Lct	C	T	1: 128,327,685	V207I	probably benign	Het
Marf1	C	A	16: 14,151,176	L144F	probably damaging	Het
Morc2b	A	T	17: 33,136,982	Y605*	probably null	Het
Mtus1	G	T	8: 41,002,361	L87I	possibly damaging	Het
Muc2	A	G	7: 141,748,971	Y17C	probably damaging	Het
Myf5	T	C	10: 107,485,918	D5G	possibly damaging	Het
Nasp	C	T	4: 116,602,157	V375M	probably damaging	Het
Nr1h2	A	T	7: 44,552,265		probably null	Het
Nrg2	T	C	18: 36,022,415	Q447R	probably benign	Het
Ntn5	G	A	7: 45,686,313	G56D	probably damaging	Het
Oasl2	A	G	5: 114,910,912	R138G	probably benign	Het
Olfr1209	A	T	2: 88,909,893	C167S	possibly damaging	Het
Olfr1489	T	A	19: 13,633,140	F10I	probably damaging	Het
Olfr827	T	C	10: 130,210,338	Y264C	probably damaging	Het
Ppp1r15a	T	C	7: 45,525,000	E128G	probably damaging	Het
Prpf19	T	C	19: 10,897,808		probably benign	Het
Ptpn3	T	A	4: 57,270,118	T15S	probably benign	Het
R3hdm2	G	A	10: 127,495,106	C818Y	probably damaging	Het
Rad51d	A	G	11: 82,889,998	V39A	possibly damaging	Het
Rptor	A	T	11: 119,872,367	T926S	probably benign	Het
Rwdd4a	G	A	8: 47,542,707	D41N	probably damaging	Het
Sephs1	A	G	2: 4,899,560	T250A	probably benign	Het
Ssbp3	T	C	4: 107,046,388	S334P	probably damaging	Het
Suco	A	G	1: 161,876,305		probably benign	Het
Synj1	T	C	16: 90,964,631	K649R	possibly damaging	Het
Tdp2	C	T	13: 24,840,448	H243Y	possibly damaging	Het
Tinag	A	G	9: 76,996,882		probably benign	Het
Trerf1	T	C	17: 47,316,662		noncoding transcript	Het
Trip10	T	C	17: 57,262,349		probably benign	Het
Tsen54	A	T	11: 115,822,030	S131C	probably damaging	Het
Unc5c	A	T	3: 141,818,067	R794*	probably null	Het
Vmn2r59	A	T	7: 42,047,008	Y103*	probably null	Het
Washc5	A	G	15: 59,352,530	V460A	probably benign	Het
Whamm	A	G	7: 81,594,015	T358A	probably benign	Het
Xlr4b	C	T	X: 73,218,671		probably benign	Het
Zbbx	C	T	3: 75,085,562		probably benign	Het
Zdhhc23	G	A	16: 43,973,703	P203S	probably benign	Het
Zfp27	T	A	7: 29,896,425	E38D	possibly damaging	Het

Other mutations in Pcdhb5

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00504:Pcdhb5	APN	18	37322109	missense	probably damaging	1.00
IGL00895:Pcdhb5	APN	18	37320983	missense	probably benign	0.42
IGL00896:Pcdhb5	APN	18	37322785	intron	probably null
IGL01385:Pcdhb5	APN	18	37322214	missense	probably benign	0.00
IGL01619:Pcdhb5	APN	18	37322939	missense	probably damaging	1.00
IGL01712:Pcdhb5	APN	18	37321253	missense	probably damaging	1.00
IGL01716:Pcdhb5	APN	18	37321022	missense	probably benign
IGL01719:Pcdhb5	APN	18	37321022	missense	probably benign
IGL01720:Pcdhb5	APN	18	37321022	missense	probably benign
IGL01723:Pcdhb5	APN	18	37321022	missense	probably benign
IGL01724:Pcdhb5	APN	18	37321022	missense	probably benign
IGL01839:Pcdhb5	APN	18	37321449	missense	probably damaging	0.98
IGL01884:Pcdhb5	APN	18	37321334	missense	probably benign	0.00
IGL01962:Pcdhb5	APN	18	37321040	missense	probably damaging	1.00
IGL02088:Pcdhb5	APN	18	37321959	missense	probably benign	0.11
IGL02299:Pcdhb5	APN	18	37320890	missense	probably benign
IGL02444:Pcdhb5	APN	18	37321050	missense	probably benign	0.01
IGL03372:Pcdhb5	APN	18	37320660	missense	probably benign	0.22
R0034:Pcdhb5	UTSW	18	37322084	missense	probably damaging	1.00
R0047:Pcdhb5	UTSW	18	37321268	missense	possibly damaging	0.87
R0466:Pcdhb5	UTSW	18	37322543	missense	probably damaging	1.00
R0471:Pcdhb5	UTSW	18	37321306	nonsense	probably null
R0565:Pcdhb5	UTSW	18	37320767	missense	possibly damaging	0.91
R0646:Pcdhb5	UTSW	18	37321622	missense	probably benign
R1014:Pcdhb5	UTSW	18	37322250	missense	probably damaging	1.00
R1617:Pcdhb5	UTSW	18	37321402	nonsense	probably null
R1676:Pcdhb5	UTSW	18	37320752	missense	probably benign	0.01
R1774:Pcdhb5	UTSW	18	37322672	missense	probably damaging	0.99
R1826:Pcdhb5	UTSW	18	37321469	nonsense	probably null
R1854:Pcdhb5	UTSW	18	37322340	missense	possibly damaging	0.94
R2355:Pcdhb5	UTSW	18	37322116	missense	probably benign
R4290:Pcdhb5	UTSW	18	37322681	missense	possibly damaging	0.90
R4292:Pcdhb5	UTSW	18	37322681	missense	possibly damaging	0.90
R4293:Pcdhb5	UTSW	18	37322681	missense	possibly damaging	0.90
R4294:Pcdhb5	UTSW	18	37322681	missense	possibly damaging	0.90
R4295:Pcdhb5	UTSW	18	37322681	missense	possibly damaging	0.90
R4391:Pcdhb5	UTSW	18	37322736	missense	possibly damaging	0.88
R4411:Pcdhb5	UTSW	18	37321997	missense	possibly damaging	0.80
R4480:Pcdhb5	UTSW	18	37320752	missense	probably benign	0.43
R4852:Pcdhb5	UTSW	18	37322471	missense	probably benign	0.04
R5121:Pcdhb5	UTSW	18	37321117	missense	probably benign	0.11
R5133:Pcdhb5	UTSW	18	37320890	missense	probably benign
R5630:Pcdhb5	UTSW	18	37321155	missense	possibly damaging	0.88
R5833:Pcdhb5	UTSW	18	37321102	missense	probably damaging	0.99
R5896:Pcdhb5	UTSW	18	37322679	nonsense	probably null
R5942:Pcdhb5	UTSW	18	37320785	nonsense	probably null
R5945:Pcdhb5	UTSW	18	37321470	missense	probably benign	0.08
R5970:Pcdhb5	UTSW	18	37321773	missense	probably damaging	1.00
R6045:Pcdhb5	UTSW	18	37321575	missense	probably damaging	1.00
R6054:Pcdhb5	UTSW	18	37321080	missense	probably damaging	0.98
R6147:Pcdhb5	UTSW	18	37320726	missense	probably damaging	1.00
R6152:Pcdhb5	UTSW	18	37322833	nonsense	probably null
R6193:Pcdhb5	UTSW	18	37322027	missense	probably damaging	1.00
R6397:Pcdhb5	UTSW	18	37321505	missense	probably benign	0.08
R6505:Pcdhb5	UTSW	18	37320880	missense	probably benign	0.00
R6608:Pcdhb5	UTSW	18	37321823	missense	probably damaging	0.98
R6737:Pcdhb5	UTSW	18	37322670	missense	probably damaging	1.00
R7146:Pcdhb5	UTSW	18	37321356	missense	probably damaging	1.00
R7162:Pcdhb5	UTSW	18	37321686	missense	probably benign	0.16
R7584:Pcdhb5	UTSW	18	37322372	missense	possibly damaging	0.90

Predicted Primers

PCR Primer
(F):5'- GCTAGACGACAATGACAATGCGCC -3'
(R):5'- TGAACTCACCAGTCCCAGATTCTCC -3'

Sequencing Primer
(F):5'- CTGGATACCTGGTCACCAAG -3'
(R):5'- CCTGTTAGACACATGTCATACTGG -3'

Posted On

2013-04-16