Mutagenetix > Incidental Mutation

Incidental Mutation 'R0646:Pcdhb5'

57228

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb5

Ensembl Gene

ENSMUSG00000063687

Gene Name

protocadherin beta 5

Synonyms

Pcdhb4A, PcdhbE

MMRRC Submission

038831-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.096) question?

Stock #

R0646 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37320381-37323915 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37321622 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 352 (T352A)

Ref Sequence

ENSEMBL: ENSMUSP00000077389 (fasta)

Gene Model

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

AlphaFold

Q91XZ5

Predicted Effect

probably benign
Transcript: ENSMUST00000078271
AA Change: T352A

PolyPhen 2 Score 0.000 (Sensitivity: 1.00; Specificity: 0.00)

SMART Domains

Protein: ENSMUSP00000077389
Gene: ENSMUSG00000063687
AA Change: T352A

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

0.1711

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.4%
20x: 95.7%

Validation Efficiency

95% (123/130)

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: 125 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610010F05Rik	C	T	11: 23,575,491	R716H	probably damaging	Het
4930432E11Rik	C	T	7: 29,561,285		noncoding transcript	Het
A430078G23Rik	T	C	8: 3,386,959	Y250H	probably damaging	Het
Abcb11	A	G	2: 69,285,283	I579T	probably damaging	Het
Abcc9	T	C	6: 142,682,104	N400S	probably benign	Het
Adarb2	T	C	13: 8,731,819	L577P	probably damaging	Het
Agt	A	C	8: 124,557,113	N422K	probably damaging	Het
Ahnak	A	T	19: 9,013,402	K4017*	probably null	Het
Akap13	C	A	7: 75,747,746	Q2575K	probably damaging	Het
Aldh3a2	A	T	11: 61,253,715	I339K	probably damaging	Het
Alox15	G	T	11: 70,345,624	Y483*	probably null	Het
Ampd1	A	T	3: 103,099,597	I713F	probably damaging	Het
Amph	A	T	13: 19,113,116	E344V	possibly damaging	Het
Arid5b	A	G	10: 68,096,977	S1032P	probably damaging	Het
Armc8	C	A	9: 99,505,688	L393F	probably damaging	Het
Bpnt1	A	G	1: 185,345,426		probably null	Het
Cachd1	G	A	4: 100,988,221	R970H	probably damaging	Het
Cd207	T	C	6: 83,675,756	T131A	probably benign	Het
Cd83	G	A	13: 43,797,533	V54I	probably benign	Het
Cfap43	T	C	19: 47,763,676	K1086E	probably benign	Het
Cfap65	A	T	1: 74,902,169	V1837E	probably benign	Het
Clcnka	T	A	4: 141,396,606	H89L	probably benign	Het
Cnga4	T	C	7: 105,404,975	I50T	possibly damaging	Het
Cog5	A	G	12: 31,837,359		probably benign	Het
Col11a2	T	A	17: 34,059,348		probably null	Het
Col28a1	T	G	6: 8,175,291	I186L	possibly damaging	Het
Col4a2	T	A	8: 11,431,252	M808K	probably benign	Het
Copb2	A	G	9: 98,563,475		probably benign	Het
Dbnl	G	A	11: 5,795,441		probably benign	Het
Dbx2	T	C	15: 95,654,612	T51A	possibly damaging	Het
Dcp1a	A	T	14: 30,502,885	M123L	probably damaging	Het
Ddx42	T	A	11: 106,232,833	F217I	probably benign	Het
Dlc1	T	C	8: 36,858,051	T367A	probably benign	Het
Dmgdh	A	T	13: 93,752,355	T834S	probably benign	Het
Dnah8	T	C	17: 30,684,173	S929P	probably damaging	Het
Dnase1l2	C	A	17: 24,441,082	V271L	possibly damaging	Het
Dsc1	T	C	18: 20,096,057	Y392C	probably damaging	Het
Edn1	T	C	13: 42,305,242		probably benign	Het
Eps8l3	T	C	3: 107,884,810	L351P	probably damaging	Het
F12	G	A	13: 55,422,483		probably benign	Het
Fam47e	T	C	5: 92,578,458		probably benign	Het
Fcrl5	C	A	3: 87,442,013	Q32K	probably benign	Het
Fndc1	C	T	17: 7,741,673	V1637I	possibly damaging	Het
Foxg1	G	T	12: 49,384,567		probably benign	Het
Frrs1	A	T	3: 116,902,421	I530F	possibly damaging	Het
Galnt5	A	T	2: 57,999,085	K232N	probably benign	Het
Ggt5	G	A	10: 75,602,648	V68M	probably damaging	Het
Gm11639	G	A	11: 104,720,501	D390N	probably benign	Het
Gm13084	A	C	4: 143,812,585	S113A	possibly damaging	Het
Gm16519	T	C	17: 70,929,106	C17R	probably benign	Het
Gm17535	A	G	9: 3,035,804	Y224C	probably null	Het
Gm884	T	A	11: 103,613,160	K485*	probably null	Het
Gm9631	T	G	11: 121,945,629	D28A	probably damaging	Het
Gpx2	T	C	12: 76,795,313	I21M	probably benign	Het
H2-Q2	T	G	17: 35,345,685	D354E	probably damaging	Het
Icam2	A	T	11: 106,380,891	I71K	probably damaging	Het
Il12a	T	C	3: 68,697,890		probably benign	Het
Insm2	C	G	12: 55,600,440	A323G	probably benign	Het
Itga1	T	C	13: 114,968,299	T1064A	probably benign	Het
Itgad	T	A	7: 128,174,004	V11E	possibly damaging	Het
Kctd15	C	T	7: 34,644,881	S115N	probably damaging	Het
Klra5	A	G	6: 129,903,564	W124R	probably damaging	Het
Kng2	T	A	16: 22,987,736	D571V	probably benign	Het
Kpna6	A	T	4: 129,650,790	F380I	probably benign	Het
Lipo1	A	T	19: 33,784,769	Y109*	probably null	Het
Man2a2	T	C	7: 80,363,197	H540R	possibly damaging	Het
Map2k4	T	C	11: 65,712,275	E188G	probably damaging	Het
Mast4	T	C	13: 102,758,744		probably benign	Het
Mbtd1	A	G	11: 93,905,212	D25G	probably damaging	Het
Med13	T	A	11: 86,331,089	Q238L	possibly damaging	Het
Mmachc	A	G	4: 116,703,654	Y215H	probably damaging	Het
Mtor	T	A	4: 148,484,354	Y1110*	probably null	Het
Nek2	A	G	1: 191,822,219	N57D	probably damaging	Het
Nek7	ACCCC	ACCC	1: 138,515,693		probably null	Het
Neo1	G	T	9: 58,931,034	T489K	probably damaging	Het
Neu1	T	A	17: 34,934,760	Y387N	probably damaging	Het
Nfasc	A	T	1: 132,608,438	C586*	probably null	Het
Nle1	G	A	11: 82,904,845	L259F	probably damaging	Het
Nrde2	G	A	12: 100,143,846	Q309*	probably null	Het
Nufip2	C	T	11: 77,686,453	H76Y	probably benign	Het
Olfr1330	A	C	4: 118,893,490	T136P	probably damaging	Het
Olfr1383	A	T	11: 49,524,578	N285I	probably damaging	Het
Olfr466	A	T	13: 65,153,063	I280F	probably damaging	Het
Olfr584	T	C	7: 103,086,151	F206S	probably damaging	Het
Olfr670	A	T	7: 104,959,811	I307N	probably benign	Het
Olfr731	A	T	14: 50,238,639	I82N	probably damaging	Het
Pcdhb7	A	T	18: 37,343,389	D526V	probably damaging	Het
Phkg1	A	T	5: 129,864,553		probably null	Het
Plg	C	T	17: 12,418,736	T744M	probably damaging	Het
Plxnd1	A	C	6: 115,958,699		probably benign	Het
Poglut1	A	T	16: 38,529,475	I312N	probably damaging	Het
Ppp1r16a	C	T	15: 76,690,799		probably benign	Het
Ppt1	A	G	4: 122,844,099	M77V	probably benign	Het
Pramel5	G	T	4: 144,271,620	T351N	probably damaging	Het
Psmb4	G	A	3: 94,884,964	R216C	probably benign	Het
Ptprd	T	C	4: 76,084,403	T699A	probably damaging	Het
Retreg3	A	T	11: 101,098,629		probably benign	Het
Scaper	G	A	9: 55,758,056	A389V	probably damaging	Het
Serinc5	G	A	13: 92,688,737	D225N	possibly damaging	Het
Slco1a1	T	G	6: 141,925,754		probably benign	Het
Snapc1	C	T	12: 73,975,032	R81C	probably damaging	Het
Sod3	A	T	5: 52,368,079	D40V	probably benign	Het
Sorcs3	C	A	19: 48,206,295	A39E	probably benign	Het
Spon1	A	T	7: 114,039,821	T761S	probably benign	Het
Syde2	A	G	3: 146,014,249		probably null	Het
Synm	T	A	7: 67,759,168	D154V	probably benign	Het
Synpo2	T	C	3: 123,114,449	E406G	probably damaging	Het
Tcea3	T	A	4: 136,248,071	L8*	probably null	Het
Tec	G	A	5: 72,823,497	L33F	probably damaging	Het
Tex15	T	A	8: 33,582,326	S2634T	possibly damaging	Het
Tg	T	A	15: 66,729,626	Y162N	probably damaging	Het
Tmem8b	G	A	4: 43,690,123	V853I	probably benign	Het
Togaram1	A	G	12: 65,021,466	K1748E	probably damaging	Het
Ttn	T	C	2: 76,898,478		probably benign	Het
Usp36	C	T	11: 118,273,021	D234N	probably damaging	Het
Usp40	G	A	1: 87,978,522	P664S	probably benign	Het
Vmn1r54	T	A	6: 90,269,653	L183H	probably benign	Het
Vmn1r58	T	G	7: 5,410,677	I185L	probably benign	Het
Wnt8a	A	T	18: 34,547,565	R328W	probably benign	Het
Yars	A	G	4: 129,213,939		probably benign	Het
Zbtb49	A	C	5: 38,200,674	M745R	probably damaging	Het
Zeb1	T	G	18: 5,759,027	F162V	probably damaging	Het
Zfp369	A	T	13: 65,297,548	H835L	probably damaging	Het
Zic5	A	G	14: 122,463,939	V460A	unknown	Het
Zp3	A	G	5: 135,984,356	N181D	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	splice site	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
R0179:Pcdhb5	UTSW	18	37322559	missense	probably damaging	1.00
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
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
R8214:Pcdhb5	UTSW	18	37321583	missense	probably benign	0.37
R8327:Pcdhb5	UTSW	18	37320900	missense	probably benign	0.00
R8676:Pcdhb5	UTSW	18	37321076	missense	probably benign	0.01
R9234:Pcdhb5	UTSW	18	37320642	missense	probably benign
R9424:Pcdhb5	UTSW	18	37321067	missense	probably damaging	1.00
R9505:Pcdhb5	UTSW	18	37321611	missense	possibly damaging	0.87
R9635:Pcdhb5	UTSW	18	37321457	missense	probably benign	0.06

Predicted Primers

PCR Primer
(F):5'- TGACTGTCTTCGCACAGGATGC -3'
(R):5'- GGTGATGTTGTACTCAGCTCTGCTC -3'

Sequencing Primer
(F):5'- TCTTCGCACAGGATGCAGATG -3'
(R):5'- AGCTCTGCTCTCTCTATCCAG -3'

Posted On

2013-07-11