Mutagenetix > Incidental Mutation

Incidental Mutation 'R2897:Pcdhb1'

260880

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb1

Ensembl Gene

ENSMUSG00000051663

Gene Name

protocadherin beta 1

Synonyms

PcdhbA

MMRRC Submission

040485-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.131) question?

Stock #

R2897 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37397991-37400578 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37399516 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Cysteine at position 489 (Y489C)

Ref Sequence

ENSEMBL: ENSMUSP00000057519 (fasta)

Gene Model

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

AlphaFold

Q91Y08

Predicted Effect

probably damaging
Transcript: ENSMUST00000052366
AA Change: Y489C

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000057519
Gene: ENSMUSG00000051663
AA Change: Y489C

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

0.6937

Coding Region Coverage

1x: 99.2%
3x: 98.7%
10x: 97.5%
20x: 95.8%

Validation Efficiency

99% (72/73)

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: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2210408I21Rik	T	C	13: 77,471,640 (GRCm39)	V1015A	probably benign	Het
4930480E11Rik	C	T	X: 77,413,868 (GRCm39)	Q198*	probably null	Het
Acap3	G	C	4: 155,989,388 (GRCm39)		probably null	Het
Adamts14	T	C	10: 61,040,689 (GRCm39)	D879G	probably damaging	Het
Akap1	A	T	11: 88,735,605 (GRCm39)	C352*	probably null	Het
Ankk1	T	A	9: 49,333,122 (GRCm39)	T121S	probably benign	Het
Ankrd6	T	C	4: 32,860,438 (GRCm39)	S2G	probably damaging	Het
Anks1	G	T	17: 28,204,337 (GRCm39)		probably null	Het
Apob	G	A	12: 8,060,356 (GRCm39)	G2946D	probably damaging	Het
Atm	A	C	9: 53,419,105 (GRCm39)	C782W	probably damaging	Het
Atp1a4	A	T	1: 172,074,257 (GRCm39)	I332N	probably damaging	Het
Bnc2	T	C	4: 84,211,152 (GRCm39)	I406V	probably damaging	Het
Cdh20	A	T	1: 104,875,199 (GRCm39)	D327V	probably damaging	Het
Cep192	T	A	18: 67,988,341 (GRCm39)		probably null	Het
Chd5	T	C	4: 152,456,572 (GRCm39)	F970L	probably damaging	Het
Coq9	T	C	8: 95,579,752 (GRCm39)	Y236H	probably damaging	Het
Csn1s2a	A	G	5: 87,929,680 (GRCm39)	H93R	unknown	Het
Cxcr2	T	C	1: 74,198,130 (GRCm39)	V208A	probably benign	Het
Cyp1b1	G	A	17: 80,021,160 (GRCm39)	T194M	probably benign	Het
Dbt	T	A	3: 116,317,061 (GRCm39)	V79E	probably damaging	Het
Dcx	A	G	X: 142,706,428 (GRCm39)		probably benign	Het
Dnm3	G	A	1: 162,113,643 (GRCm39)		probably benign	Het
Erbin	C	T	13: 104,022,705 (GRCm39)	E45K	probably damaging	Het
Fastkd1	A	G	2: 69,532,960 (GRCm39)	L469P	probably damaging	Het
Gkn3	C	T	6: 87,360,507 (GRCm39)	A163T	probably damaging	Het
Gm10271	A	G	10: 116,808,495 (GRCm39)	L7S	probably damaging	Het
Gm5087	T	C	14: 13,158,805 (GRCm38)		noncoding transcript	Het
Hid1	A	G	11: 115,241,356 (GRCm39)	S645P	probably benign	Het
Hmcn1	C	T	1: 150,678,624 (GRCm39)	C499Y	probably damaging	Het
Ifna1	C	A	4: 88,768,450 (GRCm39)	Q43K	probably benign	Het
Ikbkb	G	T	8: 23,159,693 (GRCm39)	Q432K	possibly damaging	Het
Inpp4a	A	T	1: 37,405,675 (GRCm39)	H148L	probably benign	Het
Itpr2	C	T	6: 146,074,839 (GRCm39)	R2338Q	probably benign	Het
Itpr2	A	T	6: 146,224,667 (GRCm39)	I1441N	probably damaging	Het
Krt78	T	C	15: 101,855,541 (GRCm39)	R757G	probably benign	Het
Lmx1a	T	A	1: 167,658,109 (GRCm39)		probably benign	Het
Lpxn	T	A	19: 12,796,722 (GRCm39)	S81T	probably benign	Het
Lrriq1	T	C	10: 103,063,111 (GRCm39)	N65S	probably damaging	Het
Mis18bp1	T	C	12: 65,180,360 (GRCm39)	D981G	probably benign	Het
Mpp4	T	C	1: 59,183,853 (GRCm39)	I296V	probably benign	Het
Mtrf1l	T	C	10: 5,767,565 (GRCm39)	R184G	probably benign	Het
Muc19	T	C	15: 91,822,550 (GRCm39)		noncoding transcript	Het
Myo6	T	A	9: 80,176,893 (GRCm39)		probably null	Het
Myom1	A	G	17: 71,408,215 (GRCm39)		probably benign	Het
Ndrg4	A	G	8: 96,405,014 (GRCm39)		probably null	Het
Neu2	A	G	1: 87,522,782 (GRCm39)	S72G	probably benign	Het
Nlrc4	T	A	17: 74,755,040 (GRCm39)	M59L	probably benign	Het
Nuak2	A	T	1: 132,252,791 (GRCm39)	H115L	probably damaging	Het
Oog1	T	A	12: 87,655,178 (GRCm39)	I272K	probably damaging	Het
Or10aa1	T	C	1: 173,869,699 (GRCm39)	F61S	probably damaging	Het
Or52a20	A	T	7: 103,366,749 (GRCm39)	Y316F	probably benign	Het
Pde5a	T	C	3: 122,572,651 (GRCm39)	I344T	probably benign	Het
Pip5kl1	C	A	2: 32,473,359 (GRCm39)	A332D	probably benign	Het
Pja1	T	C	X: 98,510,754 (GRCm39)	E385G	probably benign	Het
Psma6	A	T	12: 55,454,829 (GRCm39)	I53L	probably benign	Het
Ric8b	T	G	10: 84,783,761 (GRCm39)	D206E	probably benign	Het
Sardh	T	C	2: 27,079,559 (GRCm39)	D911G	probably benign	Het
Serpinb8	A	G	1: 107,534,776 (GRCm39)	T32A	unknown	Het
Shroom2	G	T	X: 151,443,035 (GRCm39)	T710K	probably benign	Het
Shroom3	G	T	5: 93,090,945 (GRCm39)	V1151F	probably damaging	Het
Slc38a7	A	G	8: 96,572,424 (GRCm39)		probably benign	Het
Stk36	T	A	1: 74,671,984 (GRCm39)	S895T	probably null	Het
Sycp3	G	A	10: 88,308,544 (GRCm39)	E205K	possibly damaging	Het
Tbc1d16	A	T	11: 119,048,654 (GRCm39)	I333N	probably damaging	Het
Tectb	C	G	19: 55,169,431 (GRCm39)		probably benign	Het
Tmeff1	T	A	4: 48,658,831 (GRCm39)	Y101*	probably null	Het
Tns2	C	T	15: 102,017,369 (GRCm39)	R281C	probably damaging	Het
Ttn	T	A	2: 76,549,500 (GRCm39)	T23399S	probably damaging	Het
Vipas39	A	G	12: 87,289,297 (GRCm39)	V389A	possibly damaging	Het
Vps41	T	C	13: 18,994,598 (GRCm39)		probably benign	Het
Zfp329	A	T	7: 12,544,413 (GRCm39)	H370Q	probably damaging	Het
Zfp37	C	T	4: 62,110,014 (GRCm39)	G350D	probably damaging	Het

Other mutations in Pcdhb1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01547:Pcdhb1	APN	18	37,400,395 (GRCm39)	missense	probably benign	0.06
IGL01622:Pcdhb1	APN	18	37,399,366 (GRCm39)	missense	possibly damaging	0.73
IGL01623:Pcdhb1	APN	18	37,399,366 (GRCm39)	missense	possibly damaging	0.73
IGL01663:Pcdhb1	APN	18	37,400,186 (GRCm39)	missense	possibly damaging	0.83
IGL01665:Pcdhb1	APN	18	37,400,450 (GRCm39)	missense	probably benign	0.01
IGL01780:Pcdhb1	APN	18	37,399,575 (GRCm39)	missense	probably damaging	1.00
IGL02121:Pcdhb1	APN	18	37,398,838 (GRCm39)	missense	probably benign	0.06
IGL02468:Pcdhb1	APN	18	37,399,231 (GRCm39)	missense	probably benign	0.21
IGL02602:Pcdhb1	APN	18	37,399,849 (GRCm39)	missense	probably damaging	1.00
K3955:Pcdhb1	UTSW	18	37,399,026 (GRCm39)	missense	probably damaging	1.00
R0242:Pcdhb1	UTSW	18	37,399,788 (GRCm39)	missense	probably benign	0.17
R0242:Pcdhb1	UTSW	18	37,399,788 (GRCm39)	missense	probably benign	0.17
R0329:Pcdhb1	UTSW	18	37,400,077 (GRCm39)	missense	possibly damaging	0.59
R0627:Pcdhb1	UTSW	18	37,398,774 (GRCm39)	missense	probably damaging	1.00
R0848:Pcdhb1	UTSW	18	37,400,475 (GRCm39)	missense	probably benign	0.00
R1187:Pcdhb1	UTSW	18	37,398,597 (GRCm39)	missense	probably damaging	1.00
R1290:Pcdhb1	UTSW	18	37,398,283 (GRCm39)	missense	possibly damaging	0.54
R1928:Pcdhb1	UTSW	18	37,399,233 (GRCm39)	nonsense	probably null
R1957:Pcdhb1	UTSW	18	37,398,760 (GRCm39)	missense	probably damaging	1.00
R2898:Pcdhb1	UTSW	18	37,399,516 (GRCm39)	missense	probably damaging	1.00
R3037:Pcdhb1	UTSW	18	37,398,166 (GRCm39)	missense	probably damaging	1.00
R4193:Pcdhb1	UTSW	18	37,400,199 (GRCm39)	missense	probably damaging	0.99
R4291:Pcdhb1	UTSW	18	37,398,470 (GRCm39)	missense	probably damaging	1.00
R4308:Pcdhb1	UTSW	18	37,399,714 (GRCm39)	missense	probably benign	0.00
R4332:Pcdhb1	UTSW	18	37,398,583 (GRCm39)	missense	probably damaging	1.00
R4606:Pcdhb1	UTSW	18	37,398,581 (GRCm39)	nonsense	probably null
R4637:Pcdhb1	UTSW	18	37,398,802 (GRCm39)	missense	possibly damaging	0.95
R5159:Pcdhb1	UTSW	18	37,399,416 (GRCm39)	missense	possibly damaging	0.89
R5207:Pcdhb1	UTSW	18	37,399,515 (GRCm39)	missense	probably damaging	1.00
R5211:Pcdhb1	UTSW	18	37,399,704 (GRCm39)	missense	probably benign	0.06
R5273:Pcdhb1	UTSW	18	37,398,766 (GRCm39)	missense	probably benign	0.23
R5335:Pcdhb1	UTSW	18	37,400,308 (GRCm39)	missense	probably benign	0.00
R5398:Pcdhb1	UTSW	18	37,399,207 (GRCm39)	missense	probably damaging	1.00
R5452:Pcdhb1	UTSW	18	37,398,811 (GRCm39)	missense	possibly damaging	0.94
R5837:Pcdhb1	UTSW	18	37,398,880 (GRCm39)	missense	possibly damaging	0.57
R5882:Pcdhb1	UTSW	18	37,400,230 (GRCm39)	missense	probably benign	0.05
R5947:Pcdhb1	UTSW	18	37,399,726 (GRCm39)	missense	possibly damaging	0.74
R6109:Pcdhb1	UTSW	18	37,398,306 (GRCm39)	missense	possibly damaging	0.69
R7052:Pcdhb1	UTSW	18	37,399,582 (GRCm39)	missense	probably damaging	1.00
R7082:Pcdhb1	UTSW	18	37,400,044 (GRCm39)	missense	probably damaging	0.99
R7137:Pcdhb1	UTSW	18	37,400,445 (GRCm39)	missense	possibly damaging	0.69
R7229:Pcdhb1	UTSW	18	37,399,740 (GRCm39)	missense	probably damaging	1.00
R7392:Pcdhb1	UTSW	18	37,398,171 (GRCm39)	missense	possibly damaging	0.95
R7993:Pcdhb1	UTSW	18	37,400,044 (GRCm39)	missense	probably damaging	1.00
R8704:Pcdhb1	UTSW	18	37,399,402 (GRCm39)	missense	possibly damaging	0.51
R9498:Pcdhb1	UTSW	18	37,398,516 (GRCm39)	missense	probably damaging	0.99
R9703:Pcdhb1	UTSW	18	37,399,019 (GRCm39)	missense	probably damaging	1.00
R9757:Pcdhb1	UTSW	18	37,400,302 (GRCm39)	missense	probably benign	0.24
T0970:Pcdhb1	UTSW	18	37,399,026 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- ATGGATACTGGACCACCCAATC -3'
(R):5'- ATTGTCATTGTCGTCCAGGACC -3'

Sequencing Primer
(F):5'- GATACTGGACCACCCAATCTGTCC -3'
(R):5'- TCTGACAGTAACTTCGCTACTCAACG -3'

Posted On

2015-01-23