Mutagenetix > Incidental Mutation

Incidental Mutation 'R7469:Pcdhb3'

579068

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb3

Ensembl Gene

ENSMUSG00000045498

Gene Name

protocadherin beta 3

Synonyms

PcdhbC

MMRRC Submission

045543-MU

Accession Numbers

Essential gene?

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

Stock #

R7469 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

37433852-37437638 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 37434388 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Lysine at position 118 (T118K)

Ref Sequence

ENSEMBL: ENSMUSP00000059180 (fasta)

Gene Model

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

AlphaFold

Q91XZ7

Predicted Effect

probably benign
Transcript: ENSMUST00000051754
AA Change: T118K

PolyPhen 2 Score 0.016 (Sensitivity: 0.95; Specificity: 0.79)

SMART Domains

Protein: ENSMUSP00000059180
Gene: ENSMUSG00000045498
AA Change: T118K

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

probably benign
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

0.1482

Coding Region Coverage

1x: 100.0%
3x: 100.0%
10x: 99.7%
20x: 99.1%

Validation Efficiency

97% (77/79)

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: 79 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcc3	A	G	11: 94,259,014 (GRCm39)	L443P	probably damaging	Het
Abtb2	T	C	2: 103,397,292 (GRCm39)	V74A	probably benign	Het
Adam5	A	T	8: 25,305,541 (GRCm39)	F66I	probably benign	Het
Aff1	T	A	5: 103,981,413 (GRCm39)	D517E	probably benign	Het
Agbl3	A	G	6: 34,791,349 (GRCm39)	K559R	probably damaging	Het
Aldh1l2	A	C	10: 83,343,969 (GRCm39)	V482G	probably damaging	Het
Ankra2	C	T	13: 98,402,882 (GRCm39)	A43V	probably benign	Het
Ankrd50	C	A	3: 38,508,342 (GRCm39)	V419F	probably damaging	Het
Arhgef16	G	A	4: 154,375,763 (GRCm39)	T77M	probably damaging	Het
Best3	T	C	10: 116,840,290 (GRCm39)	V240A	probably damaging	Het
Btbd7	T	C	12: 102,779,027 (GRCm39)	Y413C	probably damaging	Het
Bzw2	A	T	12: 36,157,550 (GRCm39)	V305E	probably damaging	Het
Cacng8	G	A	7: 3,463,621 (GRCm39)	A258T	possibly damaging	Het
Cfap157	T	C	2: 32,670,696 (GRCm39)	Y184C	probably damaging	Het
Chmp3	T	A	6: 71,556,652 (GRCm39)	V184E	possibly damaging	Het
Cst5	C	T	2: 149,247,496 (GRCm39)	L71F	probably benign	Het
Ctdspl2	A	T	2: 121,837,362 (GRCm39)	E376D	possibly damaging	Het
Cyfip1	A	G	7: 55,527,468 (GRCm39)	D200G	possibly damaging	Het
Cylc2	T	A	4: 51,227,970 (GRCm39)		probably null	Het
Cyp2c66	T	A	19: 39,172,307 (GRCm39)	F407L	probably damaging	Het
Dcp2	T	C	18: 44,529,019 (GRCm39)	F45L	probably damaging	Het
Dhx34	C	T	7: 15,950,364 (GRCm39)	R268H	probably benign	Het
Dnajc7	A	T	11: 100,482,377 (GRCm39)	M205K	probably benign	Het
Dzip3	C	T	16: 48,765,242 (GRCm39)	V491M	probably benign	Het
Farp1	T	C	14: 121,512,833 (GRCm39)	L777P	probably damaging	Het
Fchsd2	T	G	7: 100,927,863 (GRCm39)		probably null	Het
Fer1l6	A	T	15: 58,462,419 (GRCm39)		probably null	Het
Fhip1a	T	C	3: 85,580,069 (GRCm39)	D712G	probably benign	Het
Fitm2	A	G	2: 163,311,742 (GRCm39)	F157S	probably damaging	Het
Flt1	G	T	5: 147,540,379 (GRCm39)	A770E	probably damaging	Het
Flt3	T	A	5: 147,268,084 (GRCm39)	E967V	probably benign	Het
Foxc1	G	C	13: 31,992,361 (GRCm39)	A391P	unknown	Het
Foxc1	C	T	13: 31,992,362 (GRCm39)	A391V	unknown	Het
Gimap6	T	A	6: 48,679,392 (GRCm39)	T215S	probably benign	Het
Gm2431	A	T	7: 141,811,518 (GRCm39)	C129S	unknown	Het
Itpr3	T	C	17: 27,340,028 (GRCm39)	S2636P	possibly damaging	Het
Lsg1	A	G	16: 30,380,635 (GRCm39)	Y601H	probably benign	Het
Map4	G	T	9: 109,856,865 (GRCm39)		probably null	Het
Mga	T	C	2: 119,733,527 (GRCm39)	M125T	probably damaging	Het
Mxi1	A	G	19: 53,360,091 (GRCm39)	D271G	probably damaging	Het
Ndst3	T	A	3: 123,465,310 (GRCm39)	T221S	possibly damaging	Het
Neto1	T	A	18: 86,516,813 (GRCm39)	S377T	probably benign	Het
Nkx6-2	T	C	7: 139,161,555 (GRCm39)	E210G	probably damaging	Het
Nos2	G	T	11: 78,843,797 (GRCm39)	V915F	possibly damaging	Het
Nrros	G	A	16: 31,963,030 (GRCm39)	A329V	probably benign	Het
Numb	T	C	12: 83,850,578 (GRCm39)	K211E	probably benign	Het
Nup210	T	A	6: 90,995,874 (GRCm39)	I1671F	probably benign	Het
Or12j3	G	A	7: 139,953,050 (GRCm39)	L158F	possibly damaging	Het
Or4c106	T	A	2: 88,682,847 (GRCm39)	D184E	probably benign	Het
Or4c31	T	A	2: 88,291,691 (GRCm39)	H2Q	probably benign	Het
Pcdh15	A	T	10: 74,481,812 (GRCm39)	M386L	probably benign	Het
Pcdhb8	A	T	18: 37,489,011 (GRCm39)	I230F	probably damaging	Het
Peli2	G	A	14: 48,488,015 (GRCm39)	V120I	probably benign	Het
Pramel15	T	A	4: 144,099,673 (GRCm39)	Q364L	probably damaging	Het
Pramel7	T	A	2: 87,321,748 (GRCm39)	M96L	probably benign	Het
Prex2	T	A	1: 11,355,293 (GRCm39)	S1531R	probably damaging	Het
Prpf31	A	G	7: 3,636,392 (GRCm39)	T138A	possibly damaging	Het
Psme4	C	T	11: 30,752,837 (GRCm39)	T175I	probably benign	Het
Rasgrf2	A	G	13: 92,165,530 (GRCm39)		probably null	Het
Rps19	T	A	7: 24,589,190 (GRCm39)	*146K	probably null	Het
Rsu1	T	C	2: 13,082,371 (GRCm39)	N260S	probably benign	Het
Serpina3k	T	C	12: 104,311,594 (GRCm39)	C391R	not run	Het
Sipa1l1	T	G	12: 82,467,438 (GRCm39)		probably null	Het
Snd1	T	A	6: 28,626,126 (GRCm39)	Y394N	probably damaging	Het
Spaca4	A	T	7: 45,374,831 (GRCm39)	V57E	probably damaging	Het
Spata31d1b	A	G	13: 59,863,278 (GRCm39)	Y142C	probably benign	Het
Sptbn2	A	G	19: 4,795,146 (GRCm39)	K1535E	probably benign	Het
Srcin1	A	G	11: 97,425,435 (GRCm39)	S541P	probably damaging	Het
Tc2n	A	T	12: 101,631,934 (GRCm39)	F308I	probably damaging	Het
Tdrd5	T	C	1: 156,090,475 (GRCm39)	D857G	probably benign	Het
Timm22	A	G	11: 76,298,134 (GRCm39)	D35G	probably benign	Het
Tram1l1	C	A	3: 124,114,889 (GRCm39)	H16Q	probably benign	Het
Uggt1	T	C	1: 36,190,814 (GRCm39)	Y1382C	probably damaging	Het
Usp32	G	T	11: 84,879,379 (GRCm39)	D1443E	possibly damaging	Het
Uty	A	T	Y: 1,131,072 (GRCm39)	C1046S	possibly damaging	Het
Wdr31	T	A	4: 62,375,768 (GRCm39)	Q230L	probably damaging	Het
Wnt8b	C	A	19: 44,500,001 (GRCm39)	T196K	possibly damaging	Het
Xpo4	A	T	14: 57,835,436 (GRCm39)	H628Q	probably benign	Het
Zfp780b	C	T	7: 27,663,382 (GRCm39)	S391N	probably benign	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
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
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'- GGGCTTCGTAATAGCCAATTTAGC -3'
(R):5'- TGGGAGAGACCGTGTAGTTC -3'

Sequencing Primer
(F):5'- TAGCCAATTTAGCGACGGATCTG -3'
(R):5'- AGACCGTGTAGTTCTGGAGTCC -3'

Posted On

2019-10-07