Mutagenetix > Incidental Mutation

Incidental Mutation 'R1713:Pcdhb3'

190822

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb3

Ensembl Gene

ENSMUSG00000045498

Gene Name

protocadherin beta 3

Synonyms

PcdhbC

MMRRC Submission

039746-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.064) question?

Stock #

R1713 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37433852-37437638 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 37436375 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Aspartic acid at position 780 (E780D)

Ref Sequence

ENSEMBL: ENSMUSP00000059180 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000051754] [ENSMUST00000056712] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91XZ7

Predicted Effect

probably benign
Transcript: ENSMUST00000051754
AA Change: E780D

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

SMART Domains

Protein: ENSMUSP00000059180
Gene: ENSMUSG00000045498
AA Change: E780D

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: ENSMUST00000056712

SMART Domains

Protein: ENSMUSP00000059770
Gene: ENSMUSG00000045689

Domain	Start	End	E-Value	Type
CA	54	131	1.66e0	SMART
CA	155	240	1.07e-19	SMART
CA	264	344	6.03e-28	SMART
CA	367	448	2.57e-22	SMART
CA	472	558	3.36e-26	SMART
CA	588	669	3.48e-10	SMART
Pfam:Cadherin_C_2	685	768	1e-25	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

0.0898

Coding Region Coverage

1x: 99.1%
3x: 98.5%
10x: 96.7%
20x: 93.6%

Validation Efficiency

98% (96/98)

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: 90 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4921539E11Rik	T	A	4: 103,127,964 (GRCm39)	I54F	possibly damaging	Het
Ackr1	A	T	1: 173,159,916 (GRCm39)	H134Q	probably benign	Het
Agtr1b	A	T	3: 20,370,473 (GRCm39)	F44L	probably benign	Het
Ahnak	G	A	19: 8,989,173 (GRCm39)	D3486N	possibly damaging	Het
Akap9	T	C	5: 4,089,345 (GRCm39)		probably null	Het
Anks6	T	A	4: 47,039,726 (GRCm39)	Q495L	probably benign	Het
Arpp21	A	G	9: 111,896,237 (GRCm39)	S684P	probably damaging	Het
Ash1l	A	G	3: 88,983,531 (GRCm39)	E2911G	probably damaging	Het
Avpi1	C	T	19: 42,113,248 (GRCm39)	E70K	probably damaging	Het
Btbd17	G	T	11: 114,686,650 (GRCm39)	P9T	probably benign	Het
C4b	A	G	17: 34,948,245 (GRCm39)		probably benign	Het
Carm1	T	C	9: 21,497,785 (GRCm39)	V385A	probably damaging	Het
Casd1	A	G	6: 4,624,104 (GRCm39)	D299G	probably damaging	Het
Clca3a1	T	A	3: 144,730,307 (GRCm39)	K179N	probably benign	Het
Col1a2	T	C	6: 4,538,691 (GRCm39)	S1204P	unknown	Het
Col24a1	C	T	3: 145,072,624 (GRCm39)	Q780*	probably null	Het
Cxadr	C	A	16: 78,131,133 (GRCm39)	N216K	probably damaging	Het
Daam1	C	T	12: 71,942,656 (GRCm39)	T40I	unknown	Het
Dab2	C	T	15: 6,459,182 (GRCm39)	P365S	possibly damaging	Het
Dnah1	A	T	14: 31,001,139 (GRCm39)	I2402N	probably damaging	Het
Dscaml1	T	A	9: 45,663,988 (GRCm39)	S1954R	possibly damaging	Het
Dync2h1	T	C	9: 7,131,891 (GRCm39)	T1639A	probably benign	Het
Ebf1	A	T	11: 44,815,393 (GRCm39)	I336F	probably damaging	Het
Ebna1bp2	A	G	4: 118,482,881 (GRCm39)	N290S	possibly damaging	Het
Gabra2	A	G	5: 71,171,906 (GRCm39)	I110T	probably benign	Het
Galk2	A	G	2: 125,773,210 (GRCm39)	N203S	probably benign	Het
Gria4	T	C	9: 4,424,448 (GRCm39)	T806A	probably benign	Het
Impg2	A	G	16: 56,080,889 (GRCm39)	T789A	probably benign	Het
Itga6	A	G	2: 71,617,546 (GRCm39)	T22A	probably benign	Het
Itgb4	T	A	11: 115,894,315 (GRCm39)	I1312N	probably damaging	Het
Kdm4c	A	G	4: 74,216,721 (GRCm39)	D160G	probably benign	Het
Kdr	A	G	5: 76,129,127 (GRCm39)	V173A	probably benign	Het
Kif14	T	C	1: 136,455,202 (GRCm39)	S1575P	probably benign	Het
Lcp1	G	A	14: 75,436,884 (GRCm39)		probably null	Het
Lipe	C	A	7: 25,084,750 (GRCm39)	S516I	probably damaging	Het
Lrrc61	G	A	6: 48,545,708 (GRCm39)	R177Q	possibly damaging	Het
Macf1	A	G	4: 123,272,487 (GRCm39)	I6429T	probably damaging	Het
Map3k4	C	T	17: 12,468,458 (GRCm39)	E1012K	probably benign	Het
Map3k5	T	C	10: 19,986,593 (GRCm39)	F936L	possibly damaging	Het
Mllt3	A	T	4: 87,701,901 (GRCm39)	N497K	probably damaging	Het
Moxd1	G	A	10: 24,157,394 (GRCm39)	G342D	probably damaging	Het
Mtdh	A	C	15: 34,114,985 (GRCm39)	Q202H	possibly damaging	Het
Nav1	A	G	1: 135,522,972 (GRCm39)		probably benign	Het
Nop56	T	C	2: 130,119,886 (GRCm39)	V109A	possibly damaging	Het
Obscn	T	C	11: 58,970,712 (GRCm39)	D2540G	probably damaging	Het
Omg	T	C	11: 79,393,679 (GRCm39)	I60V	probably benign	Het
Or10q12	A	T	19: 13,746,659 (GRCm39)	T318S	probably benign	Het
Or12e9	A	T	2: 87,202,290 (GRCm39)	Y138F	probably damaging	Het
Osbpl5	G	A	7: 143,248,110 (GRCm39)	H652Y	probably damaging	Het
Parvb	T	C	15: 84,182,192 (GRCm39)		probably benign	Het
Pik3c3	A	G	18: 30,456,639 (GRCm39)	D723G	possibly damaging	Het
Prkdc	T	C	16: 15,612,958 (GRCm39)	V3172A	probably benign	Het
Psme4	G	T	11: 30,756,310 (GRCm39)	W272L	probably damaging	Het
Rem1	G	A	2: 152,476,455 (GRCm39)	V238M	probably damaging	Het
Rhobtb1	A	C	10: 69,108,601 (GRCm39)	S434R	probably benign	Het
Rhobtb1	G	C	10: 69,108,602 (GRCm39)	S434T	possibly damaging	Het
Rnf8	T	C	17: 29,853,735 (GRCm39)	F413S	probably damaging	Het
Rpn2	A	G	2: 157,156,888 (GRCm39)	N497S	probably damaging	Het
Rsbn1l	G	T	5: 21,156,488 (GRCm39)	P99Q	probably benign	Het
Serpinb3b	A	T	1: 107,083,164 (GRCm39)	M246K	probably benign	Het
Sgsm2	T	C	11: 74,787,652 (GRCm39)	E19G	probably null	Het
Shank1	A	G	7: 43,969,161 (GRCm39)	H352R	unknown	Het
Slc17a7	A	G	7: 44,819,728 (GRCm39)	I177V	probably benign	Het
Slc28a2	T	A	2: 122,281,494 (GRCm39)	F228I	probably damaging	Het
Slc35b4	C	T	6: 34,147,484 (GRCm39)	V35I	probably benign	Het
Slc38a1	T	C	15: 96,476,641 (GRCm39)	I407V	probably damaging	Het
Slc39a13	A	G	2: 90,893,442 (GRCm39)	V326A	probably damaging	Het
Slc44a5	T	C	3: 153,944,743 (GRCm39)	L120P	probably damaging	Het
Slfn3	T	C	11: 83,104,140 (GRCm39)	I214T	probably damaging	Het
Slitrk3	A	C	3: 72,957,024 (GRCm39)	S583A	probably benign	Het
Snx14	T	C	9: 88,297,728 (GRCm39)	Y180C	probably damaging	Het
Sorl1	T	A	9: 41,907,538 (GRCm39)	K1483I	probably benign	Het
Ssrp1	C	A	2: 84,871,104 (GRCm39)	H247N	probably damaging	Het
Stk39	A	T	2: 68,137,460 (GRCm39)		probably benign	Het
Syde1	C	T	10: 78,421,530 (GRCm39)	G674R	probably damaging	Het
Tent4a	A	T	13: 69,651,170 (GRCm39)	I565N	probably benign	Het
Themis3	G	A	17: 66,862,848 (GRCm39)	S370L	probably benign	Het
Tll1	T	A	8: 64,554,907 (GRCm39)	N259Y	probably damaging	Het
Tnip2	T	G	5: 34,661,175 (GRCm39)		probably benign	Het
Top2b	T	C	14: 16,409,823 (GRCm38)	V830A	probably benign	Het
Trpm8	T	A	1: 88,292,802 (GRCm39)	N934K	probably damaging	Het
Ttc14	A	G	3: 33,857,069 (GRCm39)	Y179C	probably damaging	Het
Ttn	T	G	2: 76,573,965 (GRCm39)	I17316L	possibly damaging	Het
Tufm	T	C	7: 126,086,871 (GRCm39)	V52A	probably benign	Het
Vamp8	T	A	6: 72,365,270 (GRCm39)	N20I	probably benign	Het
Vmn1r170	A	T	7: 23,306,288 (GRCm39)	H230L	probably benign	Het
Vmn2r50	T	G	7: 9,771,731 (GRCm39)	T657P	probably damaging	Het
Xirp2	G	A	2: 67,342,762 (GRCm39)	G1668R	probably benign	Het
Zik1	C	A	7: 10,224,311 (GRCm39)	R262L	possibly damaging	Het
Zscan25	T	G	5: 145,220,501 (GRCm39)	Y99D	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
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
R4917:Pcdhb3	UTSW	18	37,435,452 (GRCm39)	missense	probably damaging	0.99
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'- TCCAAAACGACGTGGACTTGCTC -3'
(R):5'- GGAGAGAGGTGTGCTAGATTTTACAGC -3'

Sequencing Primer
(F):5'- CCAGAGCAGCTTCTATGGGTG -3'
(R):5'- GTGCTAGATTTTACAGCTCTCAGAC -3'

Posted On

2014-05-14