Mutagenetix > Incidental Mutation

Incidental Mutation 'R4780:Pcdha6'

366458

Institutional Source

Beutler Lab

Gene Symbol

Pcdha6

Ensembl Gene

ENSMUSG00000103707

Gene Name

protocadherin alpha 6

Synonyms

Cnr2, Crnr2

MMRRC Submission

041993-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.172) question?

Stock #

R4780 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37100684-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 37102906 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Phenylalanine at position 700 (I700F)

Ref Sequence

ENSEMBL: ENSMUSP00000141587 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192503] [ENSMUST00000193389] [ENSMUST00000193777] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000193839] [ENSMUST00000192512] [ENSMUST00000192631] [ENSMUST00000195590]

AlphaFold

Q91Y14

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

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: 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: ENSMUST00000192168

SMART Domains

Protein: ENSMUSP00000142293
Gene: ENSMUSG00000103092

Domain	Start	End	E-Value	Type
CA	21	131	2.2e-2	SMART
CA	155	240	2.05e-21	SMART
CA	264	348	8.81e-21	SMART
CA	372	453	2.01e-24	SMART
CA	477	563	1.42e-24	SMART
CA	591	673	1.63e-15	SMART
transmembrane domain	693	715	N/A	INTRINSIC
low complexity region	902	926	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192178

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 damaging
Transcript: ENSMUST00000193389
AA Change: I700F

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707
AA Change: I700F

Domain	Start	End	E-Value	Type
CA	21	131	5.67e-2	SMART
CA	155	240	4.72e-21	SMART
CA	264	348	1.9e-25	SMART
CA	372	453	3.31e-25	SMART
CA	477	563	1.42e-24	SMART
CA	594	676	5.91e-13	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000193777
AA Change: I700F

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707
AA Change: I700F

Domain	Start	End	E-Value	Type
CA	21	131	5.67e-2	SMART
CA	155	240	4.72e-21	SMART
CA	264	348	1.9e-25	SMART
CA	372	453	3.31e-25	SMART
CA	477	563	1.42e-24	SMART
CA	594	676	5.91e-13	SMART
low complexity region	914	938	N/A	INTRINSIC

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

Predicted Effect

probably benign
Transcript: ENSMUST00000194751

SMART Domains

Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707

Domain	Start	End	E-Value	Type
low complexity region	15	21	N/A	INTRINSIC
Pfam:Cadherin_2	29	112	4.5e-32	PFAM

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

probably benign
Transcript: ENSMUST00000192512

SMART Domains

Protein: ENSMUSP00000141408
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	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: ENSMUST00000192631

SMART Domains

Protein: ENSMUSP00000142156
Gene: ENSMUSG00000104318

Domain	Start	End	E-Value	Type
CA	21	131	2.58e-2	SMART
CA	155	240	4.27e-19	SMART
CA	264	348	1.42e-24	SMART
CA	372	453	9.36e-25	SMART
CA	477	563	1.42e-24	SMART
CA	594	671	4.03e-6	SMART
transmembrane domain	696	718	N/A	INTRINSIC
low complexity region	905	929	N/A	INTRINSIC

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

0.6920

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 97.0%
20x: 94.6%

Validation Efficiency

98% (107/109)

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: 105 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1110002E22Rik	A	G	3: 137,771,131 (GRCm39)	N107D	probably benign	Het
4833413E03Rik	A	C	17: 31,777,738 (GRCm39)		noncoding transcript	Het
4931429L15Rik	G	T	9: 46,220,144 (GRCm39)	H129Q	possibly damaging	Het
A730018C14Rik	A	G	12: 112,382,069 (GRCm39)		noncoding transcript	Het
Abcc6	T	A	7: 45,646,115 (GRCm39)	K791N	probably benign	Het
Adcy4	T	G	14: 56,012,493 (GRCm39)	Q550P	probably benign	Het
Add3	C	A	19: 53,223,223 (GRCm39)	A325E	possibly damaging	Het
Agbl4	T	A	4: 111,514,528 (GRCm39)	I513N	possibly damaging	Het
Agfg1	C	A	1: 82,864,108 (GRCm39)	T392K	probably damaging	Het
Akna	C	A	4: 63,297,491 (GRCm39)	M854I	probably benign	Het
Ankrd44	T	C	1: 54,802,916 (GRCm39)	N194S	probably benign	Het
Anks1b	A	G	10: 89,709,594 (GRCm39)	K21E	probably damaging	Het
Ap1s3	A	G	1: 79,586,889 (GRCm39)	F154L	probably benign	Het
Apbb2	T	A	5: 66,520,160 (GRCm39)	N477I	probably damaging	Het
Apobec3	T	C	15: 79,783,225 (GRCm39)	C101R	possibly damaging	Het
Arnt	G	T	3: 95,395,696 (GRCm39)	V410F	probably damaging	Het
Arsg	G	A	11: 109,424,839 (GRCm39)	R270H	possibly damaging	Het
B3gnt7	T	A	1: 86,232,992 (GRCm39)	D79E	probably damaging	Het
Cd44	G	T	2: 102,691,910 (GRCm39)	A126D	probably damaging	Het
Cd69	A	G	6: 129,248,318 (GRCm39)	I56T	probably damaging	Het
Cep120	G	A	18: 53,857,608 (GRCm39)	P286S	probably benign	Het
Ces2a	T	C	8: 105,463,840 (GRCm39)	F184S	probably damaging	Het
Chrng	A	G	1: 87,135,246 (GRCm39)	N185S	probably damaging	Het
Cldn6	A	T	17: 23,900,221 (GRCm39)	M62L	probably benign	Het
Cntn6	T	A	6: 104,822,745 (GRCm39)	N765K	probably damaging	Het
Cspg4b	A	G	13: 113,454,392 (GRCm39)	Y146C	probably damaging	Het
Ctnnal1	T	C	4: 56,847,857 (GRCm39)	D94G	probably damaging	Het
Cyp2c69	T	C	19: 39,866,038 (GRCm39)	N185S	probably benign	Het
Depdc1a	A	G	3: 159,232,343 (GRCm39)	N698S	probably benign	Het
Dnah2	A	T	11: 69,364,697 (GRCm39)	I1986N	probably damaging	Het
Dnah7b	A	G	1: 46,392,174 (GRCm39)	E3845G	probably benign	Het
Dpysl3	C	T	18: 43,487,867 (GRCm39)	V159I	probably benign	Het
Dync1h1	T	C	12: 110,627,630 (GRCm39)	Y4047H	probably damaging	Het
E130308A19Rik	C	T	4: 59,691,057 (GRCm39)	P297L	probably benign	Het
E2f5	A	G	3: 14,652,379 (GRCm39)	T72A	probably benign	Het
Ephb6	G	T	6: 41,593,073 (GRCm39)	R437L	probably damaging	Het
Erbb4	T	C	1: 68,337,473 (GRCm39)	H615R	probably damaging	Het
Erbin	T	C	13: 104,020,714 (GRCm39)	T82A	probably damaging	Het
Eri2	T	C	7: 119,384,903 (GRCm39)	N533D	probably benign	Het
Fkbp9	A	G	6: 56,827,701 (GRCm39)	N174S	probably damaging	Het
Fsbp	C	T	4: 11,583,709 (GRCm39)	T136I	possibly damaging	Het
Fubp3	C	A	2: 31,473,223 (GRCm39)	D47E	probably damaging	Het
Gm21850	G	A	2: 153,898,419 (GRCm39)		noncoding transcript	Het
Gm5141	T	A	13: 62,922,764 (GRCm39)	Y135F	unknown	Het
Gm7353	T	A	7: 3,160,725 (GRCm39)		noncoding transcript	Het
Gm9925	T	C	18: 74,198,344 (GRCm39)		probably benign	Het
Greb1l	T	C	18: 10,541,792 (GRCm39)	S1180P	probably benign	Het
H2ac11	G	A	13: 22,227,079 (GRCm39)	Q7*	probably null	Het
Ift70a2	A	C	2: 75,807,920 (GRCm39)	C197W	probably benign	Het
Kiz	A	G	2: 146,731,166 (GRCm39)	T192A	possibly damaging	Het
Klhl24	T	A	16: 19,925,708 (GRCm39)	C79S	probably damaging	Het
Map3k11	A	G	19: 5,740,966 (GRCm39)	H231R	probably damaging	Het
Mbd4	C	A	6: 115,826,345 (GRCm39)	R194S	probably benign	Het
Mettl21e	A	C	1: 44,250,303 (GRCm39)	S34R	probably benign	Het
Mrps5	T	C	2: 127,440,161 (GRCm39)	V245A	probably benign	Het
Mtrf1	T	C	14: 79,639,128 (GRCm39)	Y87H	probably benign	Het
Myh15	T	C	16: 48,940,420 (GRCm39)	I790T	probably benign	Het
Necab1	T	G	4: 14,989,248 (GRCm39)	I176L	probably benign	Het
Nfkb2	T	A	19: 46,298,361 (GRCm39)	L555Q	probably damaging	Het
Nhlrc3	T	A	3: 53,365,988 (GRCm39)	E168D	probably benign	Het
Nlrp5	T	A	7: 23,135,203 (GRCm39)	C949S	probably damaging	Het
Nup155	C	A	15: 8,187,187 (GRCm39)	A1372E	probably benign	Het
Nynrin	G	T	14: 56,100,720 (GRCm39)	R170L	probably damaging	Het
Ogfrl1	T	A	1: 23,409,402 (GRCm39)	N275Y	probably damaging	Het
Olr1	A	T	6: 129,465,839 (GRCm39)	S56T	probably damaging	Het
Or4k52	A	G	2: 111,611,190 (GRCm39)	D175G	probably damaging	Het
Or5aq1	C	T	2: 86,966,221 (GRCm39)	S148N	probably damaging	Het
Or5b121	A	G	19: 13,507,319 (GRCm39)	N138S	probably benign	Het
Or8b48	A	G	9: 38,493,265 (GRCm39)	T231A	possibly damaging	Het
Ovol2	A	T	2: 144,173,203 (GRCm39)		probably benign	Het
Prkcz	C	T	4: 155,374,159 (GRCm39)	V86M	probably damaging	Het
Ptpn13	A	G	5: 103,734,639 (GRCm39)	T2124A	probably benign	Het
Ranbp3	G	T	17: 56,980,346 (GRCm39)		probably benign	Het
Rapgef2	A	G	3: 79,077,076 (GRCm39)		probably benign	Het
Rbl1	A	G	2: 157,016,724 (GRCm39)	V625A	probably benign	Het
Rbm38	G	T	2: 172,863,944 (GRCm39)	G38C	probably damaging	Het
Reg1	T	G	6: 78,403,333 (GRCm39)	F7C	possibly damaging	Het
Retnlg	A	T	16: 48,694,697 (GRCm39)	Q115L	possibly damaging	Het
Rhobtb1	G	A	10: 69,105,983 (GRCm39)	V183I	probably benign	Het
Rims1	T	C	1: 22,361,329 (GRCm39)	Q1186R	probably damaging	Het
Ryr1	A	G	7: 28,794,522 (GRCm39)	F1246L	possibly damaging	Het
Samm50	A	G	15: 84,094,811 (GRCm39)	N401S	possibly damaging	Het
Scn3a	T	A	2: 65,336,537 (GRCm39)	I690F	probably damaging	Het
Sdk1	A	G	5: 141,944,993 (GRCm39)	D304G	probably damaging	Het
Skint6	T	C	4: 113,093,594 (GRCm39)	Y183C	probably damaging	Het
Slamf1	A	T	1: 171,604,829 (GRCm39)	T200S	probably benign	Het
Slc34a2	C	T	5: 53,226,793 (GRCm39)	R639C	probably damaging	Het
Smap1	A	T	1: 23,892,517 (GRCm39)	M149K	probably benign	Het
Sorcs1	T	C	19: 50,132,419 (GRCm39)		probably benign	Het
Sp140	T	A	1: 85,538,549 (GRCm39)	D95E	possibly damaging	Het
Spata13	G	A	14: 60,991,356 (GRCm39)	W366*	probably null	Het
Spata31e4	C	A	13: 50,855,116 (GRCm39)	S251R	probably damaging	Het
Strip1	G	A	3: 107,534,314 (GRCm39)	T136I	probably benign	Het
Tacr1	A	T	6: 82,534,053 (GRCm39)	T360S	probably benign	Het
Tbc1d14	T	A	5: 36,728,600 (GRCm39)		probably benign	Het
Tcaf2	T	C	6: 42,604,996 (GRCm39)	Y596C	probably damaging	Het
Tspoap1	C	T	11: 87,669,269 (GRCm39)	T1454I	possibly damaging	Het
Ttn	A	T	2: 76,744,927 (GRCm39)	M5374K	probably benign	Het
Uts2r	G	A	11: 121,051,705 (GRCm39)	V190I	possibly damaging	Het
Vmn1r181	A	G	7: 23,684,008 (GRCm39)	T158A	possibly damaging	Het
Wdr35	A	T	12: 9,068,150 (GRCm39)	T778S	probably benign	Het
Xrn1	A	T	9: 95,856,797 (GRCm39)		probably benign	Het
Zfp35	A	T	18: 24,136,326 (GRCm39)	K223N	probably damaging	Het
Zfp764	T	C	7: 127,003,943 (GRCm39)	Q396R	probably benign	Het
Zfyve1	T	C	12: 83,605,421 (GRCm39)	Y11C	probably damaging	Het

Other mutations in Pcdha6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R3734:Pcdha6	UTSW	18	37,102,454 (GRCm39)	missense	probably damaging	1.00
R3859:Pcdha6	UTSW	18	37,102,984 (GRCm39)	missense	possibly damaging	0.89
R3875:Pcdha6	UTSW	18	37,101,119 (GRCm39)	missense	probably damaging	1.00
R4446:Pcdha6	UTSW	18	37,100,813 (GRCm39)	missense	probably benign	0.28
R4647:Pcdha6	UTSW	18	37,102,189 (GRCm39)	missense	probably damaging	0.98
R4659:Pcdha6	UTSW	18	37,102,292 (GRCm39)	missense	probably damaging	1.00
R4839:Pcdha6	UTSW	18	37,101,485 (GRCm39)	missense	possibly damaging	0.73
R4915:Pcdha6	UTSW	18	37,101,510 (GRCm39)	missense	probably damaging	1.00
R5011:Pcdha6	UTSW	18	37,100,960 (GRCm39)	missense	probably damaging	1.00
R5084:Pcdha6	UTSW	18	37,102,016 (GRCm39)	missense	probably damaging	1.00
R5090:Pcdha6	UTSW	18	37,101,770 (GRCm39)	missense	probably benign	0.15
R5189:Pcdha6	UTSW	18	37,101,844 (GRCm39)	missense	probably damaging	1.00
R5652:Pcdha6	UTSW	18	37,101,889 (GRCm39)	splice site	probably null
R5773:Pcdha6	UTSW	18	37,102,643 (GRCm39)	missense	probably benign	0.00
R5890:Pcdha6	UTSW	18	37,102,121 (GRCm39)	missense	possibly damaging	0.94
R6135:Pcdha6	UTSW	18	37,102,269 (GRCm39)	missense	probably damaging	1.00
R6276:Pcdha6	UTSW	18	37,102,820 (GRCm39)	splice site	probably null
R6346:Pcdha6	UTSW	18	37,101,113 (GRCm39)	missense	probably damaging	1.00
R6889:Pcdha6	UTSW	18	37,101,396 (GRCm39)	missense	probably damaging	1.00
R7295:Pcdha6	UTSW	18	37,101,189 (GRCm39)	missense	probably damaging	1.00
R7776:Pcdha6	UTSW	18	37,103,034 (GRCm39)	missense	probably benign	0.27
R7944:Pcdha6	UTSW	18	37,101,965 (GRCm39)	missense	possibly damaging	0.55
R7950:Pcdha6	UTSW	18	37,102,479 (GRCm39)	missense	probably damaging	1.00
R8371:Pcdha6	UTSW	18	37,102,920 (GRCm39)	nonsense	probably null
R8513:Pcdha6	UTSW	18	37,102,229 (GRCm39)	missense	probably damaging	1.00
R8549:Pcdha6	UTSW	18	37,101,594 (GRCm39)	missense	possibly damaging	0.83
R8735:Pcdha6	UTSW	18	37,101,203 (GRCm39)	missense	possibly damaging	0.55
R8827:Pcdha6	UTSW	18	37,102,802 (GRCm39)	missense	probably damaging	1.00
R8881:Pcdha6	UTSW	18	37,101,484 (GRCm39)	missense	probably damaging	1.00
R9094:Pcdha6	UTSW	18	37,101,593 (GRCm39)	missense	probably damaging	0.98
R9357:Pcdha6	UTSW	18	37,102,226 (GRCm39)	missense	probably benign	0.16
Z1088:Pcdha6	UTSW	18	37,102,270 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TACACGGGCGAGATCAGTAC -3'
(R):5'- GTGGTCCCTCTCCAGAACAAAC -3'

Sequencing Primer
(F):5'- AGATCAGTACCACGCGTGC -3'
(R):5'- AGAACAAACCTTCTGTCTCCTCTG -3'

Posted On

2015-12-21