Mutagenetix > Incidental Mutation

Incidental Mutation 'R5331:Pcdha4'

423286

Institutional Source

Beutler Lab

Gene Symbol

Pcdha4

Ensembl Gene

ENSMUSG00000104252

Gene Name

protocadherin alpha 4

Synonyms

Crnr1, Cnr1

MMRRC Submission

042913-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.161) question?

Stock #

R5331 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37085742-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 37087755 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Arginine to Histidine at position 646 (R646H)

Ref Sequence

ENSEMBL: ENSMUSP00000141408 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000193839] [ENSMUST00000195590]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000070797

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442

Domain	Start	End	E-Value	Type
CA	22	132	3.09e-2	SMART
CA	156	241	6.14e-20	SMART
CA	265	349	3.92e-27	SMART
CA	373	454	4.94e-24	SMART
CA	478	564	1e-24	SMART
CA	592	672	4.55e-14	SMART
transmembrane domain	694	716	N/A	INTRINSIC
Pfam:Cadherin_tail	797	931	5.3e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115661
AA Change: R646H

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: R646H

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: ENSMUST00000115662

SMART Domains

Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148

Domain	Start	End	E-Value	Type
CA	45	131	6.34e-2	SMART
CA	155	240	2.98e-18	SMART
CA	264	348	2.17e-29	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	5.02e-25	SMART
CA	594	675	8.16e-16	SMART
transmembrane domain	695	717	N/A	INTRINSIC
low complexity region	916	940	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192295

SMART Domains

Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252

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	568	5.38e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000192503

SMART Domains

Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312

Domain	Start	End	E-Value	Type
low complexity region	11	17	N/A	INTRINSIC
CA	42	128	3.78e-2	SMART
CA	152	237	8.94e-22	SMART
CA	261	345	3.74e-24	SMART
CA	369	450	1.09e-25	SMART
CA	474	560	1.42e-24	SMART
CA	588	670	2.96e-13	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	910	934	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192512
AA Change: R646H

PolyPhen 2 Score 0.006 (Sensitivity: 0.97; Specificity: 0.75)

SMART Domains

Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: R646H

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
low complexity region	915	939	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193839

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442

Domain	Start	End	E-Value	Type
CA	22	132	3.09e-2	SMART
CA	156	241	6.14e-20	SMART
CA	265	349	3.92e-27	SMART
CA	373	454	4.94e-24	SMART
CA	478	564	1e-24	SMART
CA	592	672	4.55e-14	SMART
transmembrane domain	694	716	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194235

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000194001

Predicted Effect

probably benign
Transcript: ENSMUST00000195590

SMART Domains

Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148

Domain	Start	End	E-Value	Type
CA	45	131	6.34e-2	SMART
CA	155	240	2.98e-18	SMART
CA	264	348	2.17e-29	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	5.02e-25	SMART
CA	594	675	8.16e-16	SMART
transmembrane domain	695	717	N/A	INTRINSIC

Meta Mutation Damage Score

0.2642

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.5%
20x: 96.0%

Validation Efficiency

100% (99/99)

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 alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 91 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A2m	A	G	6: 121,615,375 (GRCm39)	D83G	probably benign	Het
Ablim1	T	C	19: 57,143,681 (GRCm39)	T80A	probably damaging	Het
Adam6b	C	A	12: 113,454,200 (GRCm39)	P339H	possibly damaging	Het
Adgrb2	A	T	4: 129,915,995 (GRCm39)	H1505L	possibly damaging	Het
Ankrd46	G	A	15: 36,486,175 (GRCm39)	T26I	probably benign	Het
Bmpr1b	T	C	3: 141,562,176 (GRCm39)	N337S	probably damaging	Het
Ccdc47	C	T	11: 106,101,176 (GRCm39)	R162Q	probably benign	Het
Cct5	A	G	15: 31,594,448 (GRCm39)		probably benign	Het
Cdca2	T	C	14: 67,914,920 (GRCm39)	K780E	possibly damaging	Het
Cds1	T	C	5: 101,946,361 (GRCm39)	S187P	probably damaging	Het
Ces3a	G	A	8: 105,784,188 (GRCm39)	E416K	probably damaging	Het
Chd8	T	A	14: 52,439,571 (GRCm39)		probably benign	Het
Chuk	A	T	19: 44,067,394 (GRCm39)	V587E	probably damaging	Het
Clec16a	G	A	16: 10,549,543 (GRCm39)	C872Y	probably damaging	Het
Commd10	T	C	18: 47,093,497 (GRCm39)	V19A	probably damaging	Het
Ctsa	A	G	2: 164,676,229 (GRCm39)		probably benign	Het
Dnah6	T	A	6: 73,051,573 (GRCm39)	I3074F	probably damaging	Het
Dydc1	T	C	14: 40,804,320 (GRCm39)		probably null	Het
Ear-ps2	G	A	14: 44,284,517 (GRCm39)		noncoding transcript	Het
Elp1	T	C	4: 56,800,001 (GRCm39)	T42A	probably benign	Het
Enpp3	T	A	10: 24,684,058 (GRCm39)	N227I	probably damaging	Het
Fam131c	A	T	4: 141,110,141 (GRCm39)	T180S	probably benign	Het
Fam193a	C	A	5: 34,622,915 (GRCm39)		probably null	Het
Fbxo41	T	C	6: 85,456,888 (GRCm39)	E427G	probably benign	Het
Gabrr2	A	G	4: 33,082,583 (GRCm39)	K236E	possibly damaging	Het
Gm10152	A	T	7: 144,317,283 (GRCm39)		noncoding transcript	Het
Gm18025	C	T	12: 34,340,574 (GRCm39)	C173Y	probably benign	Het
Gm5414	C	A	15: 101,533,099 (GRCm39)	V443F	probably damaging	Het
Gm7334	T	C	17: 51,006,160 (GRCm39)	S149P	possibly damaging	Het
Gpaa1	T	A	15: 76,216,511 (GRCm39)		probably benign	Het
Grik2	G	A	10: 49,008,867 (GRCm39)	T740M	probably damaging	Het
Gvin3	T	C	7: 106,197,958 (GRCm39)		noncoding transcript	Het
Hdac5	T	C	11: 102,088,180 (GRCm39)	Y930C	probably damaging	Het
Hepacam2	T	C	6: 3,483,377 (GRCm39)	T211A	probably benign	Het
Herc4	G	T	10: 63,143,578 (GRCm39)	E703*	probably null	Het
Hras	T	C	7: 140,772,853 (GRCm39)	M1V	probably null	Het
Il23r	T	G	6: 67,400,479 (GRCm39)	Q617P	probably damaging	Het
Insc	T	A	7: 114,444,273 (GRCm39)	M420K	probably damaging	Het
Ints10	A	T	8: 69,273,472 (GRCm39)		probably null	Het
Kank1	A	G	19: 25,388,693 (GRCm39)	T789A	probably damaging	Het
Kat6a	T	A	8: 23,430,000 (GRCm39)	L1785Q	unknown	Het
Kcnj12	A	G	11: 60,961,012 (GRCm39)	K437E	probably benign	Het
Knl1	T	A	2: 118,900,736 (GRCm39)	D812E	possibly damaging	Het
Luc7l	C	A	17: 26,494,707 (GRCm39)	C104*	probably null	Het
Lurap1	G	A	4: 116,001,601 (GRCm39)	L31F	probably damaging	Het
Mia2	A	G	12: 59,142,598 (GRCm39)	S5G	probably benign	Het
Mon1b	C	T	8: 114,362,899 (GRCm39)	T49I	probably null	Het
Mrgprb3	T	C	7: 48,292,682 (GRCm39)	T290A	possibly damaging	Het
Ms4a20	A	G	19: 11,069,222 (GRCm39)		probably benign	Het
Mxd3	T	C	13: 55,477,071 (GRCm39)		probably benign	Het
Negr1	A	T	3: 156,774,913 (GRCm39)	K210*	probably null	Het
Nek7	A	T	1: 138,426,312 (GRCm39)		probably null	Het
Nktr	T	C	9: 121,581,834 (GRCm39)		probably benign	Het
Nrxn2	A	G	19: 6,540,111 (GRCm39)	T796A	probably damaging	Het
Nwd2	C	A	5: 63,963,859 (GRCm39)	L1148I	probably benign	Het
Or5d46	T	C	2: 88,170,332 (GRCm39)	L141P	probably damaging	Het
Osmr	G	C	15: 6,872,362 (GRCm39)	T244S	probably damaging	Het
Ovol3	T	C	7: 29,932,904 (GRCm39)	D177G	possibly damaging	Het
Pdilt	T	C	7: 119,114,147 (GRCm39)	E117G	possibly damaging	Het
Pecr	A	G	1: 72,314,005 (GRCm39)		probably benign	Het
Per3	G	T	4: 151,125,759 (GRCm39)	L187I	probably damaging	Het
Plcl2	G	A	17: 50,816,876 (GRCm39)	A81T	probably benign	Het
Polr2a	T	C	11: 69,638,101 (GRCm39)	N123D	probably benign	Het
Prex2	T	A	1: 11,210,235 (GRCm39)	D558E	possibly damaging	Het
Psma5	T	G	3: 108,175,386 (GRCm39)	V146G	possibly damaging	Het
Rgs11	A	T	17: 26,421,947 (GRCm39)	M1L	probably benign	Het
Rgsl1	T	C	1: 153,678,038 (GRCm39)	N130S	probably benign	Het
Rhbg	T	A	3: 88,152,775 (GRCm39)	T313S	probably benign	Het
Ripply2	T	A	9: 86,897,691 (GRCm39)		probably benign	Het
Scap	T	C	9: 110,210,701 (GRCm39)	V1011A	probably benign	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Scarf1	G	A	11: 75,406,406 (GRCm39)	G230D	probably damaging	Het
Slc17a8	A	G	10: 89,425,356 (GRCm39)		probably null	Het
Slc22a14	A	T	9: 119,059,662 (GRCm39)	L153Q	probably damaging	Het
Slc22a27	A	G	19: 7,856,820 (GRCm39)	I406T	probably benign	Het
Slc30a6	A	G	17: 74,730,190 (GRCm39)	D355G	probably benign	Het
Socs7	A	G	11: 97,268,852 (GRCm39)	D382G	possibly damaging	Het
Sphkap	A	G	1: 83,254,503 (GRCm39)	V1082A	probably benign	Het
Stox2	G	A	8: 47,866,662 (GRCm39)		probably benign	Het
Tacc2	T	C	7: 130,335,258 (GRCm39)	S524P	probably damaging	Het
Tbc1d9b	C	T	11: 50,037,140 (GRCm39)	A263V	probably benign	Het
Tekt5	C	T	16: 10,179,193 (GRCm39)	M391I	probably benign	Het
Tfap2b	A	T	1: 19,296,722 (GRCm39)	M222L	probably benign	Het
Themis2	T	C	4: 132,510,244 (GRCm39)	D652G	possibly damaging	Het
Tmem185b	A	G	1: 119,455,322 (GRCm39)		probably benign	Het
Trpv4	A	G	5: 114,773,604 (GRCm39)	Y253H	probably damaging	Het
Trpv5	G	A	6: 41,637,266 (GRCm39)	R358C	probably benign	Het
Ush2a	G	A	1: 188,460,578 (GRCm39)	G2613E	probably benign	Het
Usp25	C	A	16: 76,847,446 (GRCm39)	Q185K	probably damaging	Het
Xkr5	G	A	8: 18,983,484 (GRCm39)		probably benign	Het
Zfp541	C	T	7: 15,829,683 (GRCm39)	P1331S	probably damaging	Het

Other mutations in Pcdha4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R2570:Pcdha4	UTSW	18	37,086,665 (GRCm39)	missense	probably benign	0.00
R3114:Pcdha4	UTSW	18	37,086,603 (GRCm39)	missense	probably benign	0.02
R3115:Pcdha4	UTSW	18	37,086,603 (GRCm39)	missense	probably benign	0.02
R4154:Pcdha4	UTSW	18	37,086,639 (GRCm39)	splice site	probably null
R4381:Pcdha4	UTSW	18	37,085,928 (GRCm39)	missense	probably damaging	1.00
R4389:Pcdha4	UTSW	18	37,087,842 (GRCm39)	missense	probably benign
R4493:Pcdha4	UTSW	18	37,087,644 (GRCm39)	missense	possibly damaging	0.80
R4801:Pcdha4	UTSW	18	37,087,008 (GRCm39)	nonsense	probably null
R4802:Pcdha4	UTSW	18	37,087,008 (GRCm39)	nonsense	probably null
R4827:Pcdha4	UTSW	18	37,086,251 (GRCm39)	missense	probably damaging	1.00
R4928:Pcdha4	UTSW	18	37,087,869 (GRCm39)	missense	probably benign	0.01
R5001:Pcdha4	UTSW	18	37,088,001 (GRCm39)	missense	probably benign
R5330:Pcdha4	UTSW	18	37,087,755 (GRCm39)	missense	probably benign	0.01
R5540:Pcdha4	UTSW	18	37,087,890 (GRCm39)	missense	probably benign	0.01
R5587:Pcdha4	UTSW	18	37,087,875 (GRCm39)	missense	probably benign
R5931:Pcdha4	UTSW	18	37,087,808 (GRCm39)	missense	probably damaging	1.00
R6249:Pcdha4	UTSW	18	37,086,729 (GRCm39)	missense	probably damaging	0.99
R6427:Pcdha4	UTSW	18	37,086,786 (GRCm39)	missense	probably benign	0.00
R6612:Pcdha4	UTSW	18	37,088,031 (GRCm39)	missense	probably benign	0.00
R6616:Pcdha4	UTSW	18	37,086,953 (GRCm39)	missense	probably benign
R7030:Pcdha4	UTSW	18	37,087,080 (GRCm39)	missense	probably damaging	1.00
R7198:Pcdha4	UTSW	18	37,086,613 (GRCm39)	missense	probably damaging	0.99
R7411:Pcdha4	UTSW	18	37,086,111 (GRCm39)	missense	probably benign	0.01
R7491:Pcdha4	UTSW	18	37,087,689 (GRCm39)	missense	probably damaging	1.00
R7513:Pcdha4	UTSW	18	37,086,392 (GRCm39)	missense	probably damaging	1.00
R7544:Pcdha4	UTSW	18	37,086,776 (GRCm39)	missense	probably benign	0.05
R7735:Pcdha4	UTSW	18	37,085,961 (GRCm39)	missense	probably damaging	1.00
R7753:Pcdha4	UTSW	18	37,086,354 (GRCm39)	missense	possibly damaging	0.49
R8104:Pcdha4	UTSW	18	37,087,106 (GRCm39)	missense	probably damaging	1.00
R8239:Pcdha4	UTSW	18	37,086,128 (GRCm39)	missense	probably damaging	1.00
R8767:Pcdha4	UTSW	18	37,086,905 (GRCm39)	missense	possibly damaging	0.73
R8802:Pcdha4	UTSW	18	37,087,211 (GRCm39)	missense	possibly damaging	0.91
R8869:Pcdha4	UTSW	18	37,086,011 (GRCm39)	nonsense	probably null
R9102:Pcdha4	UTSW	18	37,087,630 (GRCm39)	missense	probably damaging	1.00
R9365:Pcdha4	UTSW	18	37,087,112 (GRCm39)	missense	possibly damaging	0.92
R9593:Pcdha4	UTSW	18	37,086,740 (GRCm39)	missense	probably benign	0.00

Predicted Primers

PCR Primer
(F):5'- TCTCTGGTGGAATCGTGAGC -3'
(R):5'- CAGATGGCAATGATCAGGTACACG -3'

Sequencing Primer
(F):5'- TCCAGATCAGTGGGTGCAG -3'
(R):5'- TGATCAGGTACACGTTGACATCC -3'

Posted On

2016-08-04