Mutagenetix > Incidental Mutations

Incidental Mutation 'R4750:Pcdhb20'

357532

Institutional Source

Beutler Lab

Gene Symbol

Pcdhb20

Ensembl Gene

ENSMUSG00000046191

Gene Name

protocadherin beta 20

Synonyms

PcdhbT, Pcdhb14

MMRRC Submission

042031-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.067) question?

Stock #

R4750 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37504264-37507822 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 37506131 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Glutamic Acid at position 570 (A570E)

Ref Sequence

ENSEMBL: ENSMUSP00000137038 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000052179] [ENSMUST00000059571] [ENSMUST00000115661] [ENSMUST00000194544]

AlphaFold

Q91XZ9

Predicted Effect

possibly damaging
Transcript: ENSMUST00000052179
AA Change: A570E

PolyPhen 2 Score 0.481 (Sensitivity: 0.89; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000137038
Gene: ENSMUSG00000046191
AA Change: A570E

Domain	Start	End	E-Value	Type
Pfam:Cadherin_2	30	112	8.3e-36	PFAM
low complexity region	136	148	N/A	INTRINSIC
CA	155	240	1.41e-19	SMART
CA	264	345	2.91e-21	SMART
CA	368	449	1.12e-22	SMART
CA	473	559	3.41e-27	SMART
CA	589	670	6.34e-13	SMART
Pfam:Cadherin_C_2	686	769	7.1e-26	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000059571

SMART Domains

Protein: ENSMUSP00000053326
Gene: ENSMUSG00000043313

Domain	Start	End	E-Value	Type
signal peptide	1	26	N/A	INTRINSIC
CA	45	131	4.8e-1	SMART
CA	155	240	6.58e-20	SMART
CA	264	345	1.03e-21	SMART
CA	368	449	4.21e-18	SMART
CA	473	559	3.36e-26	SMART
CA	589	670	6.69e-12	SMART
Pfam:Cadherin_C_2	686	769	1.9e-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

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

0.6489

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 94.9%

Validation Efficiency

97% (89/92)

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: 83 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110008P14Rik	C	T	2: 32,379,413		probably null	Het
1700074P13Rik	A	G	6: 40,921,021	W243R	probably damaging	Het
2510039O18Rik	T	A	4: 147,941,488	L155Q	probably damaging	Het
Aadac	T	C	3: 60,035,817	F48L	probably benign	Het
Aadat	T	A	8: 60,526,600	N165K	probably benign	Het
Acan	C	A	7: 79,092,718	D557E	probably damaging	Het
Adamts4	T	A	1: 171,251,066	V85D	probably benign	Het
Agt	A	G	8: 124,556,937	V481A	probably benign	Het
Angpt1	T	C	15: 42,676,401	N21D	probably benign	Het
Ankrd52	A	C	10: 128,378,089	D38A	probably damaging	Het
Ap1g2	G	T	14: 55,104,365	Q247K	probably damaging	Het
Apaf1	T	C	10: 91,060,188	R341G	probably damaging	Het
Arf2	T	C	11: 103,979,759		probably null	Het
Arhgef1	A	G	7: 24,918,576		probably benign	Het
Bbox1	T	A	2: 110,265,521	Y366F	possibly damaging	Het
Bmp3	A	G	5: 98,872,558	E280G	possibly damaging	Het
Cd109	CATTTATTTATTTATTTATTTATTTATTTATTTAT	CATTTATTTATTTATTTATTTATTTATTTATTTATTTAT	9: 78,712,500		probably benign	Het
Cdh12	T	A	15: 21,583,808	V578D	possibly damaging	Het
Cdk19	T	C	10: 40,476,199	S282P	probably damaging	Het
Cfap46	A	G	7: 139,679,323		probably null	Het
Cfhr3	T	A	1: 139,584,828		noncoding transcript	Het
Ctrc	T	A	4: 141,841,523	Y123F	probably benign	Het
Enpp4	A	G	17: 44,102,355	M96T	probably damaging	Het
Exosc10	T	A	4: 148,562,394	S154T	possibly damaging	Het
Fbxo21	G	A	5: 118,000,468	R486H	probably benign	Het
Foxj3	C	A	4: 119,616,590	A204E	probably damaging	Het
Gas6	T	G	8: 13,476,227	D237A	probably benign	Het
Gimap8	A	G	6: 48,650,427	S112G	probably benign	Het
Gm4787	T	C	12: 81,378,367	N339S	possibly damaging	Het
Gm6185	T	C	1: 161,182,363		noncoding transcript	Het
Gramd3	A	G	18: 56,432,300	E9G	probably benign	Het
Hmgxb3	A	T	18: 61,167,496	D169E	probably benign	Het
Isl2	T	A	9: 55,544,312	V162D	probably benign	Het
Kcns3	T	A	12: 11,091,654	D348V	probably damaging	Het
Kcp	G	A	6: 29,484,626	P1318S	probably benign	Het
Kif12	T	A	4: 63,167,783	Q415L	probably damaging	Het
Lama3	T	A	18: 12,504,359	H45Q	probably benign	Het
Lonp2	A	T	8: 86,631,502	K117M	probably benign	Het
Loxl4	T	A	19: 42,605,004	N243Y	probably damaging	Het
Lrif1	C	A	3: 106,735,564	Q662K	probably benign	Het
Lrrc37a	T	A	11: 103,455,480	I3187L	probably benign	Het
Lsg1	A	G	16: 30,565,449	I521T	probably damaging	Het
Mecom	T	G	3: 29,957,530	K865Q	probably damaging	Het
Myh10	T	C	11: 68,785,314	I790T	probably damaging	Het
Nek7	C	T	1: 138,498,673	S234N	probably damaging	Het
Nepro	T	C	16: 44,730,182	L179P	probably damaging	Het
Nexn	A	G	3: 152,237,722	C649R	probably damaging	Het
Nsmf	T	C	2: 25,055,026	S34P	probably damaging	Het
Olfr1140	C	T	2: 87,746,508	T104I	probably benign	Het
Olfr1339	T	A	4: 118,734,733	V68D	possibly damaging	Het
Olfr1350	A	G	7: 6,570,851	I287V	probably benign	Het
Olfr1364	A	G	13: 21,573,743	S238P	possibly damaging	Het
Olfr354	T	A	2: 36,907,716	S257T	probably benign	Het
Olfr406	T	A	11: 74,269,420	F10L	probably benign	Het
Olfr417	A	G	1: 174,368,922	I2V	probably benign	Het
Olfr685	A	T	7: 105,180,926	I144N	probably damaging	Het
Olfr702	A	G	7: 106,824,307	F73S	probably damaging	Het
P2rx5	G	T	11: 73,164,877	K53N	probably damaging	Het
Pip4k2c	T	C	10: 127,211,417	H32R	unknown	Het
Pkhd1	T	A	1: 20,524,112	D1259V	possibly damaging	Het
Plekha7	A	T	7: 116,137,311	V889E	probably damaging	Het
Polr2b	A	C	5: 77,332,039	E546D	possibly damaging	Het
Ppm1l	A	G	3: 69,549,328	T193A	probably damaging	Het
Ppp1r37	G	T	7: 19,531,520	D710E	probably benign	Het
Prdm4	A	G	10: 85,899,221	F679L	probably damaging	Het
Prkcd	A	G	14: 30,610,301	M1T	probably null	Het
Rcor3	A	G	1: 192,130,449	Y77H	unknown	Het
Rdh5	T	C	10: 128,918,366	E66G	possibly damaging	Het
Slc12a5	A	G	2: 164,982,931	M396V	probably benign	Het
Slco5a1	T	G	1: 12,879,280	T629P	probably damaging	Het
Smarca5	A	C	8: 80,733,707	N133K	probably benign	Het
Spag5	T	C	11: 78,320,052	M927T	probably benign	Het
Spint4	A	T	2: 164,700,146	D39V	probably damaging	Het
Syt6	T	A	3: 103,630,917	*512R	probably null	Het
Tmem247	T	C	17: 86,922,342	C204R	probably damaging	Het
Tmem72	A	G	6: 116,695,434	Y149H	probably damaging	Het
Trpm6	T	C	19: 18,876,064	V1816A	probably damaging	Het
Usp35	A	G	7: 97,310,339	V1008A	possibly damaging	Het
Washc4	T	C	10: 83,591,052	S1075P	probably damaging	Het
Wdr34	T	C	2: 30,033,920	T198A	probably benign	Het
Xylb	G	T	9: 119,359,313	G62*	probably null	Het
Zfp142	T	C	1: 74,572,458	E623G	probably damaging	Het
Zfp239	A	G	6: 117,871,739	Y146C	probably damaging	Het

Other mutations in Pcdhb20

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01071:Pcdhb20	APN	18	37504685	missense	possibly damaging	0.87
IGL01373:Pcdhb20	APN	18	37506568	missense	probably benign	0.10
IGL01556:Pcdhb20	APN	18	37504799	missense	possibly damaging	0.88
IGL01621:Pcdhb20	APN	18	37504807	missense	possibly damaging	0.49
IGL01768:Pcdhb20	APN	18	37506715	missense	possibly damaging	0.80
IGL01859:Pcdhb20	APN	18	37504563	missense	probably damaging	0.98
IGL02492:Pcdhb20	APN	18	37506400	missense	probably benign	0.43
IGL03057:Pcdhb20	APN	18	37504798	missense	possibly damaging	0.74
IGL02991:Pcdhb20	UTSW	18	37506211	missense	probably damaging	1.00
R0799:Pcdhb20	UTSW	18	37505885	missense	probably damaging	1.00
R1465:Pcdhb20	UTSW	18	37504697	missense	probably damaging	0.99
R1465:Pcdhb20	UTSW	18	37504697	missense	probably damaging	0.99
R2012:Pcdhb20	UTSW	18	37505074	missense	probably damaging	0.99
R2079:Pcdhb20	UTSW	18	37505171	missense	probably benign	0.07
R2350:Pcdhb20	UTSW	18	37504510	missense	probably benign	0.01
R2363:Pcdhb20	UTSW	18	37505672	missense	probably damaging	1.00
R2364:Pcdhb20	UTSW	18	37505938	missense	probably damaging	1.00
R2870:Pcdhb20	UTSW	18	37505780	missense	possibly damaging	0.82
R2870:Pcdhb20	UTSW	18	37505780	missense	possibly damaging	0.82
R4060:Pcdhb20	UTSW	18	37506164	missense	probably damaging	1.00
R4609:Pcdhb20	UTSW	18	37505796	missense	probably benign	0.02
R4897:Pcdhb20	UTSW	18	37506245	missense	possibly damaging	0.70
R4970:Pcdhb20	UTSW	18	37506771	missense	probably benign	0.00
R5098:Pcdhb20	UTSW	18	37504805	missense	probably damaging	1.00
R5616:Pcdhb20	UTSW	18	37504532	missense	probably damaging	0.97
R5890:Pcdhb20	UTSW	18	37505233	missense	probably benign	0.00
R6225:Pcdhb20	UTSW	18	37504994	missense	probably damaging	1.00
R6248:Pcdhb20	UTSW	18	37506232	missense	probably damaging	0.99
R6419:Pcdhb20	UTSW	18	37505555	missense	probably damaging	1.00
R6814:Pcdhb20	UTSW	18	37506165	missense	probably benign	0.22
R6821:Pcdhb20	UTSW	18	37506122	missense	probably damaging	1.00
R6824:Pcdhb20	UTSW	18	37505699	missense	probably benign	0.06
R6872:Pcdhb20	UTSW	18	37506165	missense	probably benign	0.22
R7040:Pcdhb20	UTSW	18	37504717	missense	probably benign	0.00
R7145:Pcdhb20	UTSW	18	37505089	missense	probably damaging	1.00
R7165:Pcdhb20	UTSW	18	37505070	missense	probably damaging	1.00
R7215:Pcdhb20	UTSW	18	37505386	missense	probably benign	0.24
R7265:Pcdhb20	UTSW	18	37505563	missense	possibly damaging	0.95
R7372:Pcdhb20	UTSW	18	37506787	missense	probably benign	0.00
R7402:Pcdhb20	UTSW	18	37504952	missense	probably benign	0.05
R7718:Pcdhb20	UTSW	18	37505651	missense	probably damaging	1.00
R7794:Pcdhb20	UTSW	18	37504432	missense	probably benign	0.00
R7842:Pcdhb20	UTSW	18	37505059	missense	possibly damaging	0.94
R8084:Pcdhb20	UTSW	18	37506173	missense	possibly damaging	0.95
R8133:Pcdhb20	UTSW	18	37506610	nonsense	probably null
R8422:Pcdhb20	UTSW	18	37504796	missense	probably damaging	1.00
R8477:Pcdhb20	UTSW	18	37505254	missense	probably benign	0.12
R8727:Pcdhb20	UTSW	18	37505384	missense	probably damaging	1.00
R8733:Pcdhb20	UTSW	18	37505384	missense	probably damaging	1.00
R8951:Pcdhb20	UTSW	18	37506093	missense	probably damaging	1.00
R9196:Pcdhb20	UTSW	18	37504971	missense	probably benign	0.00
R9384:Pcdhb20	UTSW	18	37504971	missense	probably benign	0.00
R9388:Pcdhb20	UTSW	18	37505800	missense	probably benign	0.02
Z1177:Pcdhb20	UTSW	18	37504588	missense	possibly damaging	0.95

Predicted Primers

PCR Primer
(F):5'- ACAACGGGCAGCTATTTGC -3'
(R):5'- TCCTTGACTAGCAGTACCAGC -3'

Sequencing Primer
(F):5'- GCTATTTGCGCTCAGGGC -3'
(R):5'- TTGACTAGCAGTACCAGCCTGTG -3'

Posted On

2015-11-11