Mutagenetix > Incidental Mutation

Incidental Mutation 'R7544:Pcdha4'

584125

Institutional Source

Beutler Lab

Gene Symbol

Pcdha4

Ensembl Gene

ENSMUSG00000104252

Gene Name

protocadherin alpha 4

Synonyms

Crnr1, Cnr1

MMRRC Submission

045616-MU

Accession Numbers

Essential gene?

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

Stock #

R7544 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37085742-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 37086776 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Leucine at position 320 (I320L)

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: I320L

PolyPhen 2 Score 0.223 (Sensitivity: 0.91; Specificity: 0.88)

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: I320L

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
AA Change: I320L

PolyPhen 2 Score 0.004 (Sensitivity: 0.98; Specificity: 0.59)

SMART Domains

Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: I320L

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: I320L

PolyPhen 2 Score 0.045 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: I320L

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

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

Validation Efficiency

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: 75 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933427D14Rik	C	T	11: 72,089,765 (GRCm39)	V40I	probably damaging	Het
Abcb11	T	C	2: 69,095,830 (GRCm39)	K837E	probably benign	Het
Arhgef10	T	C	8: 15,029,854 (GRCm39)	S919P	probably benign	Het
Atxn2	T	C	5: 121,919,431 (GRCm39)	S530P	probably damaging	Het
Bicc1	T	C	10: 70,792,204 (GRCm39)	E268G	possibly damaging	Het
Bnip5	G	A	17: 29,124,298 (GRCm39)	R335W	probably damaging	Het
Capn7	T	G	14: 31,062,007 (GRCm39)	L40V	probably damaging	Het
Cd28	A	T	1: 60,808,859 (GRCm39)	N191I	probably damaging	Het
Cfap69	G	A	5: 5,645,936 (GRCm39)	T588M	not run	Het
Csmd1	T	C	8: 16,142,310 (GRCm39)	E1531G	probably damaging	Het
Cyp4a14	T	A	4: 115,348,283 (GRCm39)	D398V	probably damaging	Het
Dchs2	T	C	3: 83,262,434 (GRCm39)	S2901P	probably damaging	Het
Ddx11	G	A	17: 66,433,280 (GRCm39)	G37S	probably damaging	Het
Diaph1	A	T	18: 38,026,322 (GRCm39)		probably null	Het
Ech1	T	C	7: 28,525,392 (GRCm39)	V49A	probably benign	Het
Elovl4	T	C	9: 83,665,271 (GRCm39)	Y196C	probably damaging	Het
Ern2	G	A	7: 121,772,422 (GRCm39)	L679F	probably benign	Het
Fbf1	A	T	11: 116,056,659 (GRCm39)	M17K	probably benign	Het
Flvcr1	C	A	1: 190,758,143 (GRCm39)	G50W	probably damaging	Het
Fryl	A	G	5: 73,238,382 (GRCm39)	S1455P	probably benign	Het
Fzd9	A	G	5: 135,278,716 (GRCm39)	Y390H	probably damaging	Het
Gnai3	C	T	3: 108,025,702 (GRCm39)	V126M		Het
Gpc5	T	C	14: 115,665,585 (GRCm39)	F470L	probably damaging	Het
Grin1	T	C	2: 25,195,086 (GRCm39)	N332S	probably benign	Het
Gtf3c5	T	A	2: 28,469,554 (GRCm39)	I117F	possibly damaging	Het
Hydin	A	T	8: 111,316,157 (GRCm39)	S4350C	probably benign	Het
Kcnh4	G	T	11: 100,647,906 (GRCm39)	H152Q	probably benign	Het
Kcnk12	A	T	17: 88,053,493 (GRCm39)	S390T	possibly damaging	Het
Klra9	T	G	6: 130,168,183 (GRCm39)	T28P	probably benign	Het
Lef1	T	A	3: 130,988,414 (GRCm39)	I327N	probably damaging	Het
Lin54	A	G	5: 100,633,129 (GRCm39)	V185A	possibly damaging	Het
Lrrc37	T	C	11: 103,506,274 (GRCm39)	E1898G	probably benign	Het
Lrrc4b	A	T	7: 44,111,975 (GRCm39)	I616F	probably damaging	Het
Mad2l1bp	A	G	17: 46,463,770 (GRCm39)	Y85H	possibly damaging	Het
Mars1	T	C	10: 127,147,479 (GRCm39)	E7G	probably benign	Het
Mpnd	G	A	17: 56,318,666 (GRCm39)	R225H	probably benign	Het
Muc4	T	A	16: 32,555,016 (GRCm39)	M1K	probably null	Het
Nckap5	A	G	1: 125,953,948 (GRCm39)	L868S	possibly damaging	Het
Ndst1	G	A	18: 60,830,256 (GRCm39)	T618M	probably damaging	Het
Npas1	A	T	7: 16,194,899 (GRCm39)		probably null	Het
Nr2f2	A	T	7: 70,004,499 (GRCm39)	V384D	probably damaging	Het
Or10a3b	A	G	7: 108,444,528 (GRCm39)	S230P	probably benign	Het
Or1e19	A	G	11: 73,316,596 (GRCm39)	L71P	probably damaging	Het
Or4p8	T	A	2: 88,727,705 (GRCm39)	I79F	probably damaging	Het
Paip1	T	A	13: 119,582,337 (GRCm39)	F188I	probably damaging	Het
Peg10	TCAGCATCAGGATCCCCATCAGGATGCACATCAGGATCCACATCAGGATGCACATC	T	6: 4,756,427 (GRCm39)		probably null	Het
Pgpep1	C	T	8: 71,103,168 (GRCm39)	G110R	unknown	Het
Pidd1	T	A	7: 141,020,252 (GRCm39)	H558L	possibly damaging	Het
Ppp1r1a	C	T	15: 103,439,776 (GRCm39)		probably null	Het
Pramel18	T	C	4: 101,768,599 (GRCm39)	S317P	possibly damaging	Het
Pramel51	T	A	12: 88,142,850 (GRCm39)	Y451F	probably benign	Het
Prkcg	A	G	7: 3,359,081 (GRCm39)	D96G	probably benign	Het
Prpf40b	A	G	15: 99,203,899 (GRCm39)	N154S	probably benign	Het
Psg17	A	G	7: 18,553,897 (GRCm39)	Y118H	probably benign	Het
Ptpn12	A	G	5: 21,214,509 (GRCm39)	I209T	probably damaging	Het
Reln	T	A	5: 22,181,276 (GRCm39)	K1835*	probably null	Het
Sf3b3	T	C	8: 111,564,915 (GRCm39)	M298V	probably benign	Het
Slc5a3	T	A	16: 91,874,682 (GRCm39)	N246K	probably benign	Het
Slmap	T	A	14: 26,151,001 (GRCm39)	E522D	probably damaging	Het
Slmap	C	T	14: 26,151,003 (GRCm39)	E522K	probably damaging	Het
Tcp10c	T	A	17: 13,581,260 (GRCm39)	L230Q	probably damaging	Het
Tdo2	A	G	3: 81,878,942 (GRCm39)		probably null	Het
Tet3	A	T	6: 83,381,623 (GRCm39)	W182R	probably damaging	Het
Tmem151a	T	A	19: 5,121,895 (GRCm39)	M35L	unknown	Het
Tom1l2	TTGATGATG	TTGATG	11: 60,171,040 (GRCm39)		probably benign	Het
Trak2	A	T	1: 58,960,227 (GRCm39)		probably null	Het
Trappc11	T	A	8: 47,975,449 (GRCm39)	E256D	possibly damaging	Het
Trim62	C	T	4: 128,796,346 (GRCm39)	T281I	probably benign	Het
Trip13	T	C	13: 74,081,021 (GRCm39)	E115G	probably benign	Het
Trp63	A	G	16: 25,620,837 (GRCm39)	T10A	probably benign	Het
Urah	A	T	7: 140,415,565 (GRCm39)	H11L	probably damaging	Het
Usp39	G	A	6: 72,319,891 (GRCm39)	T109I	probably damaging	Het
Wfikkn2	T	C	11: 94,128,738 (GRCm39)	T468A	probably benign	Het
Zfhx4	T	G	3: 5,477,875 (GRCm39)	S3497A	probably damaging	Het
Zfp85	C	T	13: 67,897,184 (GRCm39)	R296H	probably benign	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
R5331: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
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'- GTCAATGCCTCAGATTTAGACG -3'
(R):5'- ACTTGAAGGGGACATGACTTG -3'

Sequencing Primer
(F):5'- TCAATGCCTCAGATTTAGACGAAGGG -3'
(R):5'- ACTTGTCAGGGAGCAGGTCAC -3'

Posted On

2019-10-17