Mutagenetix > Incidental Mutation

Incidental Mutation 'R4917:Pcdhb3'

378339

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb3

Ensembl Gene

ENSMUSG00000045498

Gene Name

protocadherin beta 3

Synonyms

PcdhbC

MMRRC Submission

042519-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.062) question?

Stock #

R4917 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37433852-37437638 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 37435452 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 473 (I473F)

Ref Sequence

ENSEMBL: ENSMUSP00000059180 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000051754] [ENSMUST00000056522] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91XZ7

Predicted Effect

probably damaging
Transcript: ENSMUST00000051754
AA Change: I473F

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000059180
Gene: ENSMUSG00000045498
AA Change: I473F

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

probably benign
Transcript: ENSMUST00000056522

SMART Domains

Protein: ENSMUSP00000057921
Gene: ENSMUSG00000051599

Domain	Start	End	E-Value	Type
Pfam:Cadherin_2	32	114	5.2e-33	PFAM
CA	157	242	1.74e-19	SMART
CA	266	347	5.99e-23	SMART
CA	370	451	1.16e-20	SMART
CA	475	561	5.94e-27	SMART
CA	591	672	2.03e-11	SMART
Pfam:Cadherin_C_2	688	771	3.5e-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

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

Meta Mutation Damage Score

0.6467

Coding Region Coverage

1x: 99.0%
3x: 98.3%
10x: 96.1%
20x: 91.7%

Validation Efficiency

97% (111/114)

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: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrv1	C	T	13: 81,658,996 (GRCm39)	V2783I	probably benign	Het
Ago4	A	C	4: 126,400,635 (GRCm39)	C693G	probably damaging	Het
Apobec2	T	C	17: 48,730,153 (GRCm39)	E171G	probably benign	Het
Arfgef3	T	A	10: 18,492,638 (GRCm39)	I1258F	probably damaging	Het
Arhgef40	A	G	14: 52,227,556 (GRCm39)	E434G	probably damaging	Het
Bcas1	T	C	2: 170,220,806 (GRCm39)	D324G	probably damaging	Het
Bdp1	A	T	13: 100,191,713 (GRCm39)	V1422E	probably damaging	Het
Bfsp1	C	T	2: 143,669,391 (GRCm39)	R396Q	probably benign	Het
Bpifb9b	T	A	2: 154,156,026 (GRCm39)		probably null	Het
Cacna1s	T	A	1: 136,029,302 (GRCm39)		probably null	Het
Casp8	T	C	1: 58,866,377 (GRCm39)	F126S	probably damaging	Het
Cdh26	T	C	2: 178,091,614 (GRCm39)	S58P	probably benign	Het
Cds2	A	G	2: 132,140,398 (GRCm39)	T182A	probably damaging	Het
Cfap157	C	T	2: 32,669,965 (GRCm39)	R206H	probably benign	Het
Col7a1	G	A	9: 108,795,532 (GRCm39)	G1529E	unknown	Het
Crybg3	A	G	16: 59,350,782 (GRCm39)	F2567L	probably benign	Het
Cyp2e1	T	C	7: 140,354,527 (GRCm39)	S393P	possibly damaging	Het
D5Ertd579e	A	G	5: 36,773,160 (GRCm39)	Y412H	probably damaging	Het
Dclk2	A	T	3: 86,732,049 (GRCm39)		probably null	Het
Ddx50	A	T	10: 62,463,450 (GRCm39)	C414*	probably null	Het
Dip2c	T	A	13: 9,671,905 (GRCm39)		probably null	Het
Dmtn	G	T	14: 70,843,159 (GRCm39)	P283Q	probably damaging	Het
Dspp	C	A	5: 104,325,789 (GRCm39)	D717E	unknown	Het
Efcab11	T	C	12: 99,685,321 (GRCm39)	D151G	probably damaging	Het
Egfem1	T	C	3: 29,206,042 (GRCm39)	V93A	probably damaging	Het
Ehbp1	T	C	11: 22,096,592 (GRCm39)	D299G	probably benign	Het
Erlec1	A	G	11: 30,884,710 (GRCm39)	Y448H	possibly damaging	Het
Fer1l4	T	C	2: 155,873,220 (GRCm39)	K1287E	probably benign	Het
Fn1	A	T	1: 71,634,968 (GRCm39)		probably null	Het
Fut8	G	T	12: 77,521,818 (GRCm39)	A486S	probably damaging	Het
Gfra1	A	T	19: 58,255,522 (GRCm39)	S308R	probably damaging	Het
Gm10764	A	G	10: 87,126,579 (GRCm39)		noncoding transcript	Het
Gm5958	C	A	14: 100,073,189 (GRCm39)		noncoding transcript	Het
Gm6788	C	T	19: 28,740,664 (GRCm39)		noncoding transcript	Het
Gsdmd	A	G	15: 75,736,241 (GRCm39)	I123M	probably benign	Het
H2bc13	A	T	13: 21,900,189 (GRCm39)	V42E	probably damaging	Het
Hsf4	A	G	8: 105,999,367 (GRCm39)	E235G	probably benign	Het
Ighv1-83	T	C	12: 115,927,580 (GRCm39)	I57V	probably benign	Het
Inhca	A	C	9: 103,129,054 (GRCm39)	Y235*	probably null	Het
Inpp5f	A	T	7: 128,286,840 (GRCm39)	D573V	probably damaging	Het
Kcnj1	T	A	9: 32,308,056 (GRCm39)	L160Q	probably damaging	Het
Kcnmb3	A	T	3: 32,526,653 (GRCm39)	C179*	probably null	Het
Lrig1	A	G	6: 94,586,700 (GRCm39)	F659L	probably damaging	Het
Lrrc3	T	C	10: 77,737,253 (GRCm39)	D61G	probably benign	Het
Marchf4	T	G	1: 72,467,938 (GRCm39)	S365R	probably benign	Het
Mccc1	A	G	3: 36,051,703 (GRCm39)	L32S	probably benign	Het
Mei4	A	G	9: 81,772,216 (GRCm39)	T10A	probably benign	Het
Meis1	T	C	11: 18,959,222 (GRCm39)		probably benign	Het
Mllt1	T	C	17: 57,206,813 (GRCm39)	T344A	probably benign	Het
Mmp11	C	T	10: 75,761,419 (GRCm39)	A31T	probably damaging	Het
Mrps28	A	G	3: 8,947,614 (GRCm39)		probably benign	Het
Mthfsl	A	C	9: 88,597,550 (GRCm39)	L67V	probably damaging	Het
Ncaph2	A	G	15: 89,244,574 (GRCm39)	I11V	probably damaging	Het
Ncdn	G	A	4: 126,643,731 (GRCm39)	L364F	possibly damaging	Het
Nfat5	T	A	8: 108,051,284 (GRCm39)	D47E	probably damaging	Het
Or51g2	A	T	7: 102,622,614 (GRCm39)	I195N	possibly damaging	Het
Or5b106	T	A	19: 13,123,355 (GRCm39)	I223L	possibly damaging	Het
Or5bw2	C	T	7: 6,573,643 (GRCm39)	L218F	possibly damaging	Het
Pcdhgb8	A	T	18: 37,897,191 (GRCm39)	N754Y	probably damaging	Het
Pgbd5	C	A	8: 125,097,305 (GRCm39)	K408N	probably benign	Het
Pnisr	A	G	4: 21,859,330 (GRCm39)		probably benign	Het
Poldip3	A	T	15: 83,016,776 (GRCm39)		probably null	Het
Ppfia2	G	C	10: 106,597,978 (GRCm39)	L180F	probably damaging	Het
Psmc3	A	G	2: 90,896,317 (GRCm39)		probably benign	Het
Rab3gap1	T	A	1: 127,816,914 (GRCm39)	W58R	possibly damaging	Het
Rere	T	A	4: 150,703,601 (GRCm39)	W1528R	probably damaging	Het
Rhot1	A	G	11: 80,100,027 (GRCm39)		probably benign	Het
Rsf1	T	C	7: 97,311,612 (GRCm39)	S781P	probably damaging	Het
Rtraf	T	C	14: 19,873,784 (GRCm39)	K5R	probably damaging	Het
Rufy4	T	C	1: 74,186,822 (GRCm39)	C537R	probably damaging	Het
Ryr2	A	G	13: 11,609,872 (GRCm39)	V753A	probably damaging	Het
Ryr3	T	C	2: 112,661,530 (GRCm39)	H1820R	probably damaging	Het
Schip1	A	T	3: 68,315,818 (GRCm39)		probably benign	Het
Scin	T	A	12: 40,119,373 (GRCm39)	I552F	possibly damaging	Het
Selp	A	C	1: 163,972,475 (GRCm39)	T705P	probably damaging	Het
Sh3rf3	A	T	10: 58,842,925 (GRCm39)	D297V	probably damaging	Het
Slc24a4	T	A	12: 102,231,203 (GRCm39)		probably null	Het
Slc2a9	C	A	5: 38,574,603 (GRCm39)	L224F	probably benign	Het
Slc35e2	C	A	4: 155,700,693 (GRCm39)	P272Q	probably damaging	Het
Slf2	T	G	19: 44,960,100 (GRCm39)	D1022E	probably damaging	Het
Syne1	C	T	10: 5,007,909 (GRCm39)	C7932Y	probably damaging	Het
Tc2n	A	G	12: 101,631,954 (GRCm39)	L301P	probably damaging	Het
Tchhl1	A	G	3: 93,377,623 (GRCm39)	D109G	possibly damaging	Het
Thoc7	T	C	14: 13,953,154 (GRCm38)	I83V	probably damaging	Het
Tm4sf1	C	T	3: 57,200,448 (GRCm39)	G85S	probably damaging	Het
Tmem63a	T	A	1: 180,794,086 (GRCm39)	I541N	probably benign	Het
Tmpo	A	G	10: 90,985,411 (GRCm39)	V357A	probably damaging	Het
Unc80	T	C	1: 66,685,709 (GRCm39)	Y2278H	possibly damaging	Het
Vmn1r26	A	G	6: 57,985,808 (GRCm39)	F127S	probably damaging	Het
Vmn2r8	A	T	5: 108,945,264 (GRCm39)	M781K	probably damaging	Het
Vps36	T	G	8: 22,708,280 (GRCm39)	M348R	possibly damaging	Het
Vps45	T	C	3: 95,926,943 (GRCm39)	T535A	probably damaging	Het

Other mutations in Pcdhb3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00976:Pcdhb3	APN	18	37,436,001 (GRCm39)	missense	probably benign	0.12
IGL01568:Pcdhb3	APN	18	37,435,054 (GRCm39)	missense	possibly damaging	0.74
IGL02541:Pcdhb3	APN	18	37,435,198 (GRCm39)	missense	probably damaging	0.99
IGL02852:Pcdhb3	APN	18	37,435,150 (GRCm39)	missense	probably damaging	1.00
IGL03140:Pcdhb3	APN	18	37,434,272 (GRCm39)	missense	probably benign	0.00
IGL03336:Pcdhb3	APN	18	37,436,014 (GRCm39)	missense	possibly damaging	0.86
R0380:Pcdhb3	UTSW	18	37,435,210 (GRCm39)	missense	possibly damaging	0.48
R1558:Pcdhb3	UTSW	18	37,434,634 (GRCm39)	missense	probably damaging	1.00
R1713:Pcdhb3	UTSW	18	37,436,375 (GRCm39)	missense	probably benign
R1728:Pcdhb3	UTSW	18	37,434,931 (GRCm39)	missense	probably damaging	1.00
R1784:Pcdhb3	UTSW	18	37,434,931 (GRCm39)	missense	probably damaging	1.00
R1838:Pcdhb3	UTSW	18	37,434,370 (GRCm39)	missense	probably benign	0.00
R2079:Pcdhb3	UTSW	18	37,436,362 (GRCm39)	missense	possibly damaging	0.93
R2164:Pcdhb3	UTSW	18	37,435,239 (GRCm39)	missense	possibly damaging	0.78
R2513:Pcdhb3	UTSW	18	37,434,294 (GRCm39)	missense	probably benign	0.17
R2513:Pcdhb3	UTSW	18	37,434,292 (GRCm39)	nonsense	probably null
R2513:Pcdhb3	UTSW	18	37,434,293 (GRCm39)	missense	probably damaging	1.00
R3080:Pcdhb3	UTSW	18	37,434,535 (GRCm39)	missense	probably damaging	1.00
R3755:Pcdhb3	UTSW	18	37,435,878 (GRCm39)	missense	probably damaging	0.97
R3756:Pcdhb3	UTSW	18	37,435,878 (GRCm39)	missense	probably damaging	0.97
R3862:Pcdhb3	UTSW	18	37,436,329 (GRCm39)	missense	probably damaging	1.00
R3863:Pcdhb3	UTSW	18	37,436,329 (GRCm39)	missense	probably damaging	1.00
R3864:Pcdhb3	UTSW	18	37,436,329 (GRCm39)	missense	probably damaging	1.00
R4114:Pcdhb3	UTSW	18	37,435,093 (GRCm39)	missense	probably benign	0.03
R4895:Pcdhb3	UTSW	18	37,434,759 (GRCm39)	missense	probably damaging	1.00
R5508:Pcdhb3	UTSW	18	37,434,179 (GRCm39)	missense	probably damaging	1.00
R5779:Pcdhb3	UTSW	18	37,434,520 (GRCm39)	missense	probably benign	0.26
R5848:Pcdhb3	UTSW	18	37,434,700 (GRCm39)	missense	probably benign	0.39
R5991:Pcdhb3	UTSW	18	37,434,561 (GRCm39)	missense	probably benign	0.07
R6014:Pcdhb3	UTSW	18	37,435,706 (GRCm39)	missense	probably damaging	1.00
R6111:Pcdhb3	UTSW	18	37,435,242 (GRCm39)	missense	probably benign	0.00
R6282:Pcdhb3	UTSW	18	37,434,699 (GRCm39)	missense	probably damaging	1.00
R6339:Pcdhb3	UTSW	18	37,433,998 (GRCm39)	intron	probably benign
R6425:Pcdhb3	UTSW	18	37,435,528 (GRCm39)	missense	possibly damaging	0.64
R6860:Pcdhb3	UTSW	18	37,434,763 (GRCm39)	missense	probably benign	0.01
R6896:Pcdhb3	UTSW	18	37,434,265 (GRCm39)	missense	probably damaging	1.00
R6946:Pcdhb3	UTSW	18	37,435,672 (GRCm39)	missense	probably damaging	1.00
R7110:Pcdhb3	UTSW	18	37,435,975 (GRCm39)	missense	possibly damaging	0.87
R7236:Pcdhb3	UTSW	18	37,434,505 (GRCm39)	missense	probably damaging	1.00
R7402:Pcdhb3	UTSW	18	37,434,657 (GRCm39)	missense	probably benign
R7469:Pcdhb3	UTSW	18	37,434,388 (GRCm39)	missense	probably benign	0.02
R7723:Pcdhb3	UTSW	18	37,435,565 (GRCm39)	missense	probably damaging	0.98
R7738:Pcdhb3	UTSW	18	37,436,012 (GRCm39)	missense	probably benign	0.00
R7800:Pcdhb3	UTSW	18	37,434,974 (GRCm39)	missense	probably benign	0.00
R7817:Pcdhb3	UTSW	18	37,435,982 (GRCm39)	missense	probably benign
R8157:Pcdhb3	UTSW	18	37,436,292 (GRCm39)	missense	probably damaging	1.00
R9264:Pcdhb3	UTSW	18	37,435,166 (GRCm39)	missense	probably benign	0.03
R9482:Pcdhb3	UTSW	18	37,434,736 (GRCm39)	missense	probably damaging	1.00
R9488:Pcdhb3	UTSW	18	37,435,416 (GRCm39)	missense	possibly damaging	0.62
X0026:Pcdhb3	UTSW	18	37,434,817 (GRCm39)	missense	probably damaging	0.96
X0066:Pcdhb3	UTSW	18	37,435,392 (GRCm39)	nonsense	probably null
Z1177:Pcdhb3	UTSW	18	37,435,089 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TCAGAGCTGAGTACAACATCAC -3'
(R):5'- TCATTGTCGTCCAGCACCAC -3'

Sequencing Primer
(F):5'- TGAGTACAACATCACCATCACGG -3'
(R):5'- GGTGAGCCTCCATCTGTG -3'

Posted On

2016-04-15