Mutagenetix > Incidental Mutation

Incidental Mutation 'R1871:Pcdhb2'

210784

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb2

Ensembl Gene

ENSMUSG00000051599

Gene Name

protocadherin beta 2

Synonyms

PcdhbB

MMRRC Submission

039893-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.056) question?

Stock #

R1871 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37427893-37430667 bp(+) (GRCm39)

Type of Mutation

splice site (934 bp from exon)

DNA Base Change (assembly)

A to T at 37430408 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000141439 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000051754] [ENSMUST00000056522] [ENSMUST00000115661] [ENSMUST00000193137] [ENSMUST00000194544]

AlphaFold

Q91Y00

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

probably damaging
Transcript: ENSMUST00000056522
AA Change: N794Y

PolyPhen 2 Score 0.989 (Sensitivity: 0.72; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000057921
Gene: ENSMUSG00000051599
AA Change: N794Y

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 null
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 null
Transcript: ENSMUST00000193137

SMART Domains

Protein: ENSMUSP00000141439
Gene: ENSMUSG00000051599

Domain	Start	End	E-Value	Type
CA	13	94	1.8e-22	SMART

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

0.9698

Coding Region Coverage

1x: 97.5%
3x: 97.0%
10x: 95.6%
20x: 93.2%

Validation Efficiency

97% (87/90)

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
A930009A15Rik	A	G	10: 115,415,699 (GRCm39)		probably null	Het
Abca13	A	T	11: 9,242,134 (GRCm39)	E1332D	probably benign	Het
Abce1	G	A	8: 80,411,897 (GRCm39)	Q588*	probably null	Het
Acads	A	T	5: 115,255,701 (GRCm39)	C45S	probably damaging	Het
Adam34l	A	T	8: 44,078,132 (GRCm39)	Y697*	probably null	Het
Adamts12	T	C	15: 11,311,240 (GRCm39)	S1166P	probably benign	Het
Ano4	T	A	10: 88,828,889 (GRCm39)	I517F	probably damaging	Het
Arpc1a	T	A	5: 145,043,901 (GRCm39)	C344S	possibly damaging	Het
Blk	A	T	14: 63,613,364 (GRCm39)	S381R	possibly damaging	Het
Capn15	C	A	17: 26,183,203 (GRCm39)	W426L	probably damaging	Het
Chd6	T	C	2: 160,832,176 (GRCm39)	T999A	probably damaging	Het
Clca3a2	A	G	3: 144,503,398 (GRCm39)	Y851H	probably benign	Het
Crp	T	A	1: 172,526,172 (GRCm39)	W86R	possibly damaging	Het
Ctnnal1	G	A	4: 56,812,534 (GRCm39)	L705F	probably benign	Het
Cyp2c66	A	G	19: 39,151,858 (GRCm39)	D191G	possibly damaging	Het
Cyp4f37	A	G	17: 32,853,639 (GRCm39)	D441G	probably damaging	Het
D130040H23Rik	T	A	8: 69,755,354 (GRCm39)	I253N	probably benign	Het
Dnah5	T	A	15: 28,331,859 (GRCm39)	Y2148*	probably null	Het
Eef1g	A	T	19: 8,955,330 (GRCm39)	D393V	possibly damaging	Het
Elapor2	A	G	5: 9,468,007 (GRCm39)	E225G	probably damaging	Het
Ephx2	A	T	14: 66,322,183 (GRCm39)	I538N	probably damaging	Het
Fat4	T	A	3: 39,035,221 (GRCm39)	S2958T	possibly damaging	Het
Foxi1	A	T	11: 34,157,937 (GRCm39)	N29K	possibly damaging	Het
Gm10287	G	T	3: 148,930,373 (GRCm39)		noncoding transcript	Het
Gm10801	G	T	2: 98,494,185 (GRCm39)	S109I	probably benign	Het
Gmcl1	T	C	6: 86,674,498 (GRCm39)	D460G	probably benign	Het
Gpr158	A	G	2: 21,820,426 (GRCm39)	D641G	probably damaging	Het
Heph	C	A	X: 95,542,690 (GRCm39)	S561Y	probably benign	Het
Hgfac	A	G	5: 35,200,257 (GRCm39)	*90W	probably null	Het
Hp1bp3	C	G	4: 137,949,497 (GRCm39)	P65R	probably damaging	Het
Ighv6-4	T	A	12: 114,370,221 (GRCm39)	Y58F	probably benign	Het
Jrk	T	C	15: 74,578,412 (GRCm39)	D291G	possibly damaging	Het
Kdm4d	A	G	9: 14,375,679 (GRCm39)	Y60H	probably damaging	Het
Khdrbs3	T	C	15: 68,921,291 (GRCm39)	Y203H	probably damaging	Het
Klhl6	A	T	16: 19,775,793 (GRCm39)	V255D	possibly damaging	Het
Krt9	C	T	11: 100,081,614 (GRCm39)	R305H	probably damaging	Het
Lama2	T	G	10: 26,860,490 (GRCm39)	N2999T	probably damaging	Het
Letm2	A	G	8: 26,086,460 (GRCm39)		probably benign	Het
Lipa	A	T	19: 34,488,328 (GRCm39)	L106Q	probably damaging	Het
Llph	A	T	10: 120,067,141 (GRCm39)	N86I	probably damaging	Het
Lyst	T	A	13: 13,826,297 (GRCm39)	N1601K	probably benign	Het
Mc1r	T	A	8: 124,134,275 (GRCm39)	S9R	probably benign	Het
Mfsd14a	A	G	3: 116,434,969 (GRCm39)	I249T	probably benign	Het
Mtfp1	G	A	11: 4,044,012 (GRCm39)	R73C	probably benign	Het
Myo1a	A	G	10: 127,555,540 (GRCm39)	Q877R	probably benign	Het
Nalcn	A	C	14: 123,831,965 (GRCm39)	V103G	possibly damaging	Het
Ndst3	A	T	3: 123,355,673 (GRCm39)	F119I	probably damaging	Het
Or8k16	A	G	2: 85,520,655 (GRCm39)	N294S	probably damaging	Het
Patl1	T	C	19: 11,902,596 (GRCm39)		probably benign	Het
Pcdhb22	A	C	18: 37,652,200 (GRCm39)	T223P	probably damaging	Het
Pcdhga1	T	A	18: 37,973,143 (GRCm39)	N907K	probably damaging	Het
Pfas	T	C	11: 68,882,795 (GRCm39)	D782G	probably damaging	Het
Plpp6	T	C	19: 28,941,684 (GRCm39)	F95S	probably damaging	Het
Polr2b	T	A	5: 77,474,374 (GRCm39)		probably benign	Het
Qars1	T	G	9: 108,391,315 (GRCm39)		probably null	Het
Ranbp2	A	G	10: 58,328,383 (GRCm39)	I2800V	probably damaging	Het
Rnf213	T	C	11: 119,340,955 (GRCm39)	V3532A	probably benign	Het
Rubcnl	T	C	14: 75,279,849 (GRCm39)	S411P	possibly damaging	Het
Scn1a	C	A	2: 66,148,369 (GRCm39)	G1059W	probably damaging	Het
Sgms1	C	T	19: 32,137,282 (GRCm39)	V95I	probably benign	Het
Siglecf	A	G	7: 43,004,967 (GRCm39)	N399S	probably benign	Het
Slc29a4	T	C	5: 142,707,243 (GRCm39)	*529R	probably null	Het
Slfn9	G	T	11: 82,872,402 (GRCm39)	T778N	probably benign	Het
Sorl1	G	A	9: 41,881,021 (GRCm39)	Q2167*	probably null	Het
Stkld1	A	G	2: 26,827,985 (GRCm39)		probably benign	Het
Taar8b	T	C	10: 23,967,900 (GRCm39)	Y98C	probably damaging	Het
Tecta	G	A	9: 42,248,472 (GRCm39)	L1977F	probably damaging	Het
Tecta	G	C	9: 42,248,636 (GRCm39)	T1917R	probably damaging	Het
Topaz1	T	A	9: 122,628,544 (GRCm39)	S1544T	probably benign	Het
Tpx2	T	C	2: 152,735,523 (GRCm39)	I717T	probably damaging	Het
Tyk2	A	T	9: 21,032,737 (GRCm39)	V342E	probably damaging	Het
Ube4a	A	T	9: 44,856,235 (GRCm39)		probably null	Het
Unc80	A	T	1: 66,549,876 (GRCm39)	R711S	possibly damaging	Het
Ush2a	C	A	1: 188,558,665 (GRCm39)	D3631E	probably benign	Het
Usp34	A	G	11: 23,314,479 (GRCm39)	H807R	probably benign	Het
Vps13a	T	C	19: 16,642,028 (GRCm39)	T2200A	probably benign	Het
Wif1	A	G	10: 120,920,824 (GRCm39)	I215M	probably benign	Het
Wnk1	T	C	6: 119,928,050 (GRCm39)	T1134A	probably damaging	Het
Xxylt1	A	G	16: 30,776,235 (GRCm39)	V367A	probably damaging	Het
Zfp735	A	T	11: 73,601,412 (GRCm39)	K119*	probably null	Het

Other mutations in Pcdhb2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00430:Pcdhb2	APN	18	37,429,516 (GRCm39)	splice site	probably null
IGL01538:Pcdhb2	APN	18	37,428,375 (GRCm39)	nonsense	probably null
IGL01716:Pcdhb2	APN	18	37,429,791 (GRCm39)	missense	probably damaging	0.99
IGL01747:Pcdhb2	APN	18	37,429,356 (GRCm39)	missense	probably damaging	1.00
IGL01770:Pcdhb2	APN	18	37,429,356 (GRCm39)	missense	probably damaging	1.00
IGL01999:Pcdhb2	APN	18	37,429,890 (GRCm39)	missense	probably damaging	1.00
IGL02174:Pcdhb2	APN	18	37,429,551 (GRCm39)	missense	probably damaging	1.00
IGL02325:Pcdhb2	APN	18	37,429,733 (GRCm39)	missense	possibly damaging	0.91
IGL03148:Pcdhb2	APN	18	37,429,831 (GRCm39)	missense	probably damaging	1.00
IGL03263:Pcdhb2	APN	18	37,429,059 (GRCm39)	missense	probably damaging	1.00
R0158:Pcdhb2	UTSW	18	37,430,283 (GRCm39)	missense	probably damaging	1.00
R0512:Pcdhb2	UTSW	18	37,429,032 (GRCm39)	missense	probably damaging	1.00
R0656:Pcdhb2	UTSW	18	37,428,543 (GRCm39)	missense	probably damaging	1.00
R0670:Pcdhb2	UTSW	18	37,429,701 (GRCm39)	missense	probably damaging	1.00
R0698:Pcdhb2	UTSW	18	37,430,419 (GRCm39)	missense	probably benign	0.00
R0825:Pcdhb2	UTSW	18	37,428,710 (GRCm39)	missense	possibly damaging	0.61
R0827:Pcdhb2	UTSW	18	37,428,710 (GRCm39)	missense	possibly damaging	0.61
R0862:Pcdhb2	UTSW	18	37,428,710 (GRCm39)	missense	possibly damaging	0.61
R0863:Pcdhb2	UTSW	18	37,428,710 (GRCm39)	missense	possibly damaging	0.61
R1344:Pcdhb2	UTSW	18	37,428,710 (GRCm39)	missense	possibly damaging	0.61
R1440:Pcdhb2	UTSW	18	37,429,343 (GRCm39)	missense	probably benign	0.22
R1826:Pcdhb2	UTSW	18	37,429,038 (GRCm39)	missense	probably damaging	0.99
R1828:Pcdhb2	UTSW	18	37,429,038 (GRCm39)	missense	probably damaging	0.99
R1869:Pcdhb2	UTSW	18	37,430,408 (GRCm39)	splice site	probably null
R2292:Pcdhb2	UTSW	18	37,430,297 (GRCm39)	splice site	probably null
R3743:Pcdhb2	UTSW	18	37,429,470 (GRCm39)	missense	probably damaging	1.00
R4067:Pcdhb2	UTSW	18	37,430,367 (GRCm39)	splice site	probably null
R4127:Pcdhb2	UTSW	18	37,428,594 (GRCm39)	missense	probably damaging	0.97
R4402:Pcdhb2	UTSW	18	37,428,455 (GRCm39)	missense	probably benign	0.05
R4579:Pcdhb2	UTSW	18	37,429,168 (GRCm39)	missense	probably damaging	1.00
R4621:Pcdhb2	UTSW	18	37,428,980 (GRCm39)	missense	probably benign	0.44
R4678:Pcdhb2	UTSW	18	37,429,260 (GRCm39)	missense	probably damaging	1.00
R5143:Pcdhb2	UTSW	18	37,429,785 (GRCm39)	missense	probably damaging	1.00
R5152:Pcdhb2	UTSW	18	37,429,179 (GRCm39)	missense	probably damaging	0.97
R6552:Pcdhb2	UTSW	18	37,429,046 (GRCm39)	missense	probably benign
R6908:Pcdhb2	UTSW	18	37,429,577 (GRCm39)	missense	probably damaging	1.00
R6973:Pcdhb2	UTSW	18	37,429,416 (GRCm39)	missense	probably benign	0.03
R7143:Pcdhb2	UTSW	18	37,428,934 (GRCm39)	missense	probably benign	0.05
R7248:Pcdhb2	UTSW	18	37,429,547 (GRCm39)	missense	probably damaging	1.00
R7586:Pcdhb2	UTSW	18	37,428,857 (GRCm39)	nonsense	probably null
R7634:Pcdhb2	UTSW	18	37,428,000 (GRCm39)	intron	probably benign
R7796:Pcdhb2	UTSW	18	37,428,446 (GRCm39)	missense	possibly damaging	0.63
R7862:Pcdhb2	UTSW	18	37,429,113 (GRCm39)	missense	probably benign	0.25
R8415:Pcdhb2	UTSW	18	37,429,110 (GRCm39)	missense	probably damaging	0.97
R8950:Pcdhb2	UTSW	18	37,429,715 (GRCm39)	missense	probably damaging	1.00
R9351:Pcdhb2	UTSW	18	37,429,369 (GRCm39)	missense	probably damaging	1.00
R9360:Pcdhb2	UTSW	18	37,429,551 (GRCm39)	missense	probably damaging	1.00
R9592:Pcdhb2	UTSW	18	37,429,266 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGTCATTGCCTTGGCCTCTG -3'
(R):5'- GCAAGCAAAATTTAGATTCCTTCTTCC -3'

Sequencing Primer
(F):5'- TGGCTGCTCTATGCCCGAAG -3'
(R):5'- AATTTAGATTCCTTCTTCCACATACC -3'

Posted On

2014-06-30