Mutagenetix > Incidental Mutation

Incidental Mutation 'R0329:Pcdhb1'

25969

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb1

Ensembl Gene

ENSMUSG00000051663

Gene Name

protocadherin beta 1

Synonyms

PcdhbA

MMRRC Submission

038538-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.118) question?

Stock #

R0329 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37264938-37267525 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37267024 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 676 (D676G)

Ref Sequence

ENSEMBL: ENSMUSP00000057519 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000052366] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91Y08

Predicted Effect

possibly damaging
Transcript: ENSMUST00000052366
AA Change: D676G

PolyPhen 2 Score 0.587 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000057519
Gene: ENSMUSG00000051663
AA Change: D676G

Domain	Start	End	E-Value	Type
CA	45	131	1.04e-1	SMART
CA	155	240	1.23e-19	SMART
CA	264	345	8.4e-27	SMART
CA	369	450	5.31e-15	SMART
CA	474	560	6.27e-26	SMART
CA	590	671	6.05e-10	SMART
Pfam:Cadherin_C_2	687	772	4.7e-18	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

0.1761

Coding Region Coverage

1x: 98.9%
3x: 97.8%
10x: 95.0%
20x: 89.0%

Validation Efficiency

99% (107/108)

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: 107 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700061G19Rik	A	T	17: 56,883,631	I400F	probably benign	Het
4833423E24Rik	T	A	2: 85,518,551	R72S	probably benign	Het
4931409K22Rik	T	C	5: 24,545,785		probably null	Het
Abca13	A	T	11: 9,399,430	H3668L	probably damaging	Het
Acvr1c	T	C	2: 58,284,838	T313A	probably damaging	Het
Adam28	T	C	14: 68,617,739	K651R	probably damaging	Het
Adamtsl3	A	T	7: 82,521,990	D417V	probably damaging	Het
Adgrf4	A	T	17: 42,667,313	C380S	probably damaging	Het
AI597479	T	G	1: 43,111,117	L129R	probably benign	Het
Anpep	C	T	7: 79,838,256	E518K	probably benign	Het
Anxa7	A	C	14: 20,469,498		probably null	Het
Arhgap22	A	G	14: 33,369,417	R650G	possibly damaging	Het
Atp8a1	T	A	5: 67,812,073		probably benign	Het
Bcr	C	T	10: 75,181,634	T1209I	possibly damaging	Het
Bmpr1a	C	T	14: 34,429,777	S185N	probably benign	Het
Calcoco1	A	T	15: 102,715,763	M246K	probably benign	Het
Casp12	T	A	9: 5,345,534		probably benign	Het
Ccno	T	A	13: 112,989,996	L333Q	probably damaging	Het
Cdhr2	T	A	13: 54,734,801		probably benign	Het
Cftr	T	A	6: 18,226,097	M318K	probably null	Het
Ckmt2	T	A	13: 91,863,203	D96V	possibly damaging	Het
Cnnm1	C	T	19: 43,441,910	P489L	probably damaging	Het
Cntnap1	A	T	11: 101,188,309	D1175V	probably damaging	Het
Cpne5	A	T	17: 29,211,660	L92H	probably damaging	Het
Crcp	C	A	5: 130,042,242	Q61K	possibly damaging	Het
Dcaf8	T	A	1: 172,187,411	D414E	probably benign	Het
Ddx28	T	C	8: 106,010,245	T394A	probably benign	Het
Ddx55	T	C	5: 124,559,147	F191L	probably benign	Het
Dnaaf1	T	C	8: 119,596,017		probably benign	Het
Dnaaf2	C	A	12: 69,197,744	R181L	probably damaging	Het
Elac2	A	G	11: 64,979,310	Y67C	probably damaging	Het
Elf5	A	G	2: 103,430,420		probably benign	Het
Emcn	T	A	3: 137,416,814		probably benign	Het
Erbb4	T	C	1: 68,298,280		probably benign	Het
Erbin	C	A	13: 103,868,865	C114F	probably damaging	Het
Etfdh	T	C	3: 79,609,844	I353V	probably benign	Het
Fam172a	T	A	13: 77,761,951		probably benign	Het
Fbxl12	C	T	9: 20,638,480	G316D	probably damaging	Het
Gbf1	G	A	19: 46,272,270		probably null	Het
Gbp2b	T	G	3: 142,608,176	S406A	probably benign	Het
Gli3	T	G	13: 15,723,558	L741R	probably damaging	Het
Gmip	G	T	8: 69,810,818	S70I	probably benign	Het
Gnptab	T	C	10: 88,440,309	S1153P	probably damaging	Het
Gp1ba	A	G	11: 70,640,409		probably benign	Het
Gramd1a	T	C	7: 31,138,254	D360G	possibly damaging	Het
Hectd4	T	C	5: 121,259,864	I285T	probably benign	Het
Hrh4	A	G	18: 13,007,245		probably benign	Het
Hsp90b1	T	C	10: 86,694,155	E226G	probably damaging	Het
Hspa13	A	T	16: 75,765,130	D60E	probably damaging	Het
Htt	T	A	5: 34,817,134		probably benign	Het
Ispd	C	T	12: 36,381,838	A22V	possibly damaging	Het
Kif14	G	C	1: 136,496,026		probably benign	Het
Kit	T	G	5: 75,652,829	V888G	probably damaging	Het
Lpin3	T	C	2: 160,905,305	V827A	probably benign	Het
Lrriq4	T	C	3: 30,655,724	S406P	probably benign	Het
Man2c1	T	C	9: 57,141,183	V777A	probably benign	Het
Mcm8	A	G	2: 132,819,994	K83E	possibly damaging	Het
Mep1a	A	G	17: 43,497,898		probably null	Het
Mtor	T	A	4: 148,484,380	V1119E	probably benign	Het
Mybpc2	C	T	7: 44,509,029	A710T	possibly damaging	Het
Myo9a	C	G	9: 59,923,677	T2368S	probably damaging	Het
Nbeal1	A	G	1: 60,268,063	Y1684C	probably damaging	Het
Npm3	A	G	19: 45,749,526	F11L	probably benign	Het
Nutf2	T	A	8: 105,876,363	S37T	probably damaging	Het
Obscn	T	A	11: 59,040,441	I5790F	probably damaging	Het
Obscn	A	T	11: 59,052,506	D4833E	probably damaging	Het
Olfr1015	T	A	2: 85,785,803	C97*	probably null	Het
Olfr123	A	T	17: 37,795,989	M182L	probably benign	Het
Olfr39	T	A	9: 20,285,857	S61T	possibly damaging	Het
Olfr955	T	C	9: 39,470,556	T57A	possibly damaging	Het
Pcif1	G	T	2: 164,889,444	R466L	probably damaging	Het
Pdk1	T	C	2: 71,895,674		probably benign	Het
Phxr2	T	C	10: 99,126,117		probably benign	Het
Pidd1	A	T	7: 141,439,561		probably benign	Het
Plec	A	G	15: 76,191,418		probably null	Het
Polr1a	T	A	6: 71,966,416	C1212S	possibly damaging	Het
Pot1a	A	G	6: 25,778,831		probably benign	Het
Prdm5	T	C	6: 65,862,903		probably benign	Het
Primpol	A	T	8: 46,610,461	N53K	probably damaging	Het
Pyroxd1	A	G	6: 142,361,976	I491V	probably benign	Het
Serpinb3b	G	T	1: 107,159,703	N25K	probably damaging	Het
Slc9b1	C	T	3: 135,373,235	R218*	probably null	Het
Ssbp2	T	A	13: 91,680,579		probably null	Het
Stat4	A	G	1: 52,090,870		probably benign	Het
Steap4	T	C	5: 7,975,829	V130A	possibly damaging	Het
Stoml2	A	G	4: 43,030,238		probably null	Het
Syne2	G	T	12: 75,966,953	G2974C	probably benign	Het
Tfdp2	T	G	9: 96,306,893	F200V	probably damaging	Het
Tgm4	T	C	9: 123,048,557		probably null	Het
Tie1	C	A	4: 118,484,727	R175L	probably benign	Het
Tmem145	A	G	7: 25,308,674		probably benign	Het
Tsacc	A	G	3: 88,282,862	S94P	possibly damaging	Het
Tshz3	T	A	7: 36,770,033	D482E	probably benign	Het
Tspan33	T	C	6: 29,711,092		probably null	Het
Ugt2b35	A	G	5: 87,003,405	K290R	probably null	Het
Unc80	T	C	1: 66,674,087	L2788P	possibly damaging	Het
Usp10	T	A	8: 119,936,557	C39*	probably null	Het
Utp20	T	A	10: 88,817,979	T260S	probably benign	Het
Vmn2r118	G	T	17: 55,610,717	T265K	probably damaging	Het
Vmn2r7	C	A	3: 64,691,018	C797F	probably damaging	Het
Vmn2r98	A	C	17: 19,066,347	H369P	probably benign	Het
Vps39	A	T	2: 120,338,787	Y245N	possibly damaging	Het
Wdr27	A	G	17: 14,934,459		probably benign	Het
Ythdc2	A	G	18: 44,865,060		probably benign	Het
Zcwpw2	C	A	9: 118,014,055		noncoding transcript	Het
Zdhhc1	C	A	8: 105,483,543	A81S	probably benign	Het
Zfp729a	G	T	13: 67,620,354	H585Q	probably damaging	Het

Other mutations in Pcdhb1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01547:Pcdhb1	APN	18	37267342	missense	probably benign	0.06
IGL01622:Pcdhb1	APN	18	37266313	missense	possibly damaging	0.73
IGL01623:Pcdhb1	APN	18	37266313	missense	possibly damaging	0.73
IGL01663:Pcdhb1	APN	18	37267133	missense	possibly damaging	0.83
IGL01665:Pcdhb1	APN	18	37267397	missense	probably benign	0.01
IGL01780:Pcdhb1	APN	18	37266522	missense	probably damaging	1.00
IGL02121:Pcdhb1	APN	18	37265785	missense	probably benign	0.06
IGL02468:Pcdhb1	APN	18	37266178	missense	probably benign	0.21
IGL02602:Pcdhb1	APN	18	37266796	missense	probably damaging	1.00
K3955:Pcdhb1	UTSW	18	37265973	missense	probably damaging	1.00
R0242:Pcdhb1	UTSW	18	37266735	missense	probably benign	0.17
R0242:Pcdhb1	UTSW	18	37266735	missense	probably benign	0.17
R0627:Pcdhb1	UTSW	18	37265721	missense	probably damaging	1.00
R0848:Pcdhb1	UTSW	18	37267422	missense	probably benign	0.00
R1187:Pcdhb1	UTSW	18	37265544	missense	probably damaging	1.00
R1290:Pcdhb1	UTSW	18	37265230	missense	possibly damaging	0.54
R1928:Pcdhb1	UTSW	18	37266180	nonsense	probably null
R1957:Pcdhb1	UTSW	18	37265707	missense	probably damaging	1.00
R2897:Pcdhb1	UTSW	18	37266463	missense	probably damaging	1.00
R2898:Pcdhb1	UTSW	18	37266463	missense	probably damaging	1.00
R3037:Pcdhb1	UTSW	18	37265113	missense	probably damaging	1.00
R4193:Pcdhb1	UTSW	18	37267146	missense	probably damaging	0.99
R4291:Pcdhb1	UTSW	18	37265417	missense	probably damaging	1.00
R4308:Pcdhb1	UTSW	18	37266661	missense	probably benign	0.00
R4332:Pcdhb1	UTSW	18	37265530	missense	probably damaging	1.00
R4606:Pcdhb1	UTSW	18	37265528	nonsense	probably null
R4637:Pcdhb1	UTSW	18	37265749	missense	possibly damaging	0.95
R5159:Pcdhb1	UTSW	18	37266363	missense	possibly damaging	0.89
R5207:Pcdhb1	UTSW	18	37266462	missense	probably damaging	1.00
R5211:Pcdhb1	UTSW	18	37266651	missense	probably benign	0.06
R5273:Pcdhb1	UTSW	18	37265713	missense	probably benign	0.23
R5335:Pcdhb1	UTSW	18	37267255	missense	probably benign	0.00
R5398:Pcdhb1	UTSW	18	37266154	missense	probably damaging	1.00
R5452:Pcdhb1	UTSW	18	37265758	missense	possibly damaging	0.94
R5837:Pcdhb1	UTSW	18	37265827	missense	possibly damaging	0.57
R5882:Pcdhb1	UTSW	18	37267177	missense	probably benign	0.05
R5947:Pcdhb1	UTSW	18	37266673	missense	possibly damaging	0.74
R6109:Pcdhb1	UTSW	18	37265253	missense	possibly damaging	0.69
R7052:Pcdhb1	UTSW	18	37266529	missense	probably damaging	1.00
R7082:Pcdhb1	UTSW	18	37266991	missense	probably damaging	0.99
R7137:Pcdhb1	UTSW	18	37267392	missense	possibly damaging	0.69
R7229:Pcdhb1	UTSW	18	37266687	missense	probably damaging	1.00
R7392:Pcdhb1	UTSW	18	37265118	missense	possibly damaging	0.95
R7993:Pcdhb1	UTSW	18	37266991	missense	probably damaging	1.00
R8704:Pcdhb1	UTSW	18	37266349	missense	possibly damaging	0.51
R9498:Pcdhb1	UTSW	18	37265463	missense	probably damaging	0.99
R9703:Pcdhb1	UTSW	18	37265966	missense	probably damaging	1.00
R9757:Pcdhb1	UTSW	18	37267249	missense	probably benign	0.24
T0970:Pcdhb1	UTSW	18	37265973	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CTTTGCCCTGCAATGACCTAGTACC -3'
(R):5'- AGTTCCCGTGGCTGAGCACATATC -3'

Sequencing Primer
(F):5'- TGACCTAGTACCAAGGTCTGC -3'
(R):5'- GAGATAAGGAACCATTGCCTCTTC -3'

Posted On

2013-04-16