Mutagenetix > Incidental Mutation

Incidental Mutation 'R7753:Pcdha4'

597407

Institutional Source

Beutler Lab

Gene Symbol

Pcdha4

Ensembl Gene

ENSMUSG00000104252

Gene Name

protocadherin alpha 4

Synonyms

Crnr1, Cnr1

MMRRC Submission

045809-MU

Accession Numbers

Essential gene?

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

Stock #

R7753 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37085742-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 37086354 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Tyrosine at position 179 (S179Y)

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

possibly damaging
Transcript: ENSMUST00000115661
AA Change: S179Y

PolyPhen 2 Score 0.936 (Sensitivity: 0.80; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458
AA Change: S179Y

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 damaging
Transcript: ENSMUST00000192295
AA Change: S179Y

PolyPhen 2 Score 0.987 (Sensitivity: 0.73; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252
AA Change: S179Y

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

possibly damaging
Transcript: ENSMUST00000192512
AA Change: S179Y

PolyPhen 2 Score 0.490 (Sensitivity: 0.88; Specificity: 0.90)

SMART Domains

Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252
AA Change: S179Y

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: 100.0%
10x: 99.8%
20x: 99.2%

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: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca6	T	C	11: 110,074,933 (GRCm39)	T1377A	probably damaging	Het
AI661453	G	T	17: 47,778,439 (GRCm39)	E722*	probably null	Het
Ap2b1	A	T	11: 83,258,733 (GRCm39)	K735*	probably null	Het
Aqp4	T	C	18: 15,533,033 (GRCm39)	E20G	probably benign	Het
Atp6v1b1	G	T	6: 83,729,440 (GRCm39)	V117L	probably benign	Het
C1rb	A	G	6: 124,557,390 (GRCm39)	N509S	probably benign	Het
Cep44	A	G	8: 56,985,842 (GRCm39)	V350A	probably benign	Het
Cmya5	T	C	13: 93,234,680 (GRCm39)	Q136R	probably benign	Het
Cntrl	T	C	2: 35,001,691 (GRCm39)	S32P	probably damaging	Het
Cyp2d12	A	T	15: 82,441,164 (GRCm39)	E201V	possibly damaging	Het
Cyp4a14	G	T	4: 115,350,861 (GRCm39)	Q138K	probably damaging	Het
Dapk1	T	C	13: 60,899,007 (GRCm39)	Y826H	possibly damaging	Het
Dbh	A	G	2: 27,061,448 (GRCm39)	D294G	probably benign	Het
Ddx10	A	T	9: 53,136,904 (GRCm39)	L336Q	probably damaging	Het
Dop1a	A	G	9: 86,371,755 (GRCm39)	T149A	possibly damaging	Het
Epg5	A	G	18: 77,991,560 (GRCm39)	T86A	possibly damaging	Het
Fam171a1	A	T	2: 3,179,354 (GRCm39)	Q60L	probably damaging	Het
Farsb	T	A	1: 78,456,740 (GRCm39)	E41D	probably benign	Het
Frem1	T	C	4: 82,832,217 (GRCm39)	D1956G	probably benign	Het
Fzd4	T	A	7: 89,056,992 (GRCm39)	Y346*	probably null	Het
Fzd7	A	T	1: 59,522,641 (GRCm39)	S175C	probably benign	Het
Gdi2	A	G	13: 3,598,956 (GRCm39)	T47A	probably benign	Het
Gpr155	A	T	2: 73,212,550 (GRCm39)	H24Q	probably benign	Het
Hdac7	A	T	15: 97,698,642 (GRCm39)	N638K	possibly damaging	Het
Hdac7	G	T	15: 97,704,369 (GRCm39)	N515K	probably benign	Het
Hnrnpul2	T	C	19: 8,802,336 (GRCm39)	V401A	probably damaging	Het
Ifi27l2b	T	A	12: 103,417,519 (GRCm39)	R223*	probably null	Het
Igkv4-91	T	G	6: 68,745,761 (GRCm39)	S46R	probably benign	Het
Itk	T	A	11: 46,222,722 (GRCm39)	L582F	probably damaging	Het
Kcnab2	T	C	4: 152,481,218 (GRCm39)	I181V	probably benign	Het
Krtap5-2	GCCACAGCCTCCACAGGAGCCACAGCCTCCCTTGCAGCCCCCACAGGAACCACAGCCTCC	GCCACAGCCTCC	7: 141,729,136 (GRCm39)		probably benign	Het
Lce1m	C	A	3: 92,925,815 (GRCm39)	G41W	unknown	Het
Mapk10	T	A	5: 103,186,419 (GRCm39)	K98*	probably null	Het
Mapk8ip2	A	G	15: 89,345,856 (GRCm39)	E812G	probably damaging	Het
Mlh1	C	A	9: 111,081,931 (GRCm39)		probably null	Het
Mroh1	A	G	15: 76,317,475 (GRCm39)	D784G	possibly damaging	Het
Neo1	A	T	9: 58,863,288 (GRCm39)	D426E	probably benign	Het
Nol4	T	A	18: 23,171,659 (GRCm39)	M1L	probably benign	Het
Nr1h3	A	G	2: 91,015,370 (GRCm39)	F338S	probably damaging	Het
Oasl2	A	G	5: 115,043,118 (GRCm39)	K297E	probably benign	Het
Or10ag59	A	G	2: 87,406,141 (GRCm39)	T238A	probably benign	Het
Or10z1	C	T	1: 174,078,236 (GRCm39)	V86I	probably benign	Het
Or4f14	A	G	2: 111,742,927 (GRCm39)	I116T	probably benign	Het
Or56a5	T	C	7: 104,793,007 (GRCm39)	I164M	probably benign	Het
Or5m5	A	G	2: 85,815,060 (GRCm39)	N292S	possibly damaging	Het
Osbpl9	T	C	4: 108,990,970 (GRCm39)	T97A	possibly damaging	Het
P3h2	A	T	16: 25,789,687 (GRCm39)	Y527N	probably damaging	Het
Papss2	A	T	19: 32,597,579 (GRCm39)	H9L	probably benign	Het
Ppt1	A	T	4: 122,730,131 (GRCm39)	D28V	possibly damaging	Het
Prkcz	T	A	4: 155,357,425 (GRCm39)	Q345L	possibly damaging	Het
Prr14l	G	T	5: 32,984,597 (GRCm39)	L1633I	probably damaging	Het
Prss51	T	A	14: 64,333,376 (GRCm39)	V13D	possibly damaging	Het
Qrich2	TTGCAACACACCAGGCTGAACTGGACCTTGCTG	TTG	11: 116,347,868 (GRCm39)		probably benign	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Slc2a7	T	C	4: 150,239,141 (GRCm39)	I122T	possibly damaging	Het
Spata31e4	A	T	13: 50,855,817 (GRCm39)	D485V	probably damaging	Het
Sprr3	G	A	3: 92,364,415 (GRCm39)	P143L	probably benign	Het
Sugct	A	T	13: 17,752,104 (GRCm39)	S181T	possibly damaging	Het
Syne2	G	A	12: 76,085,697 (GRCm39)	R141Q	probably benign	Het
Taok1	T	C	11: 77,428,725 (GRCm39)	I992V	probably benign	Het
Tbc1d21	A	C	9: 58,269,306 (GRCm39)		probably null	Het
Thada	T	C	17: 84,559,818 (GRCm39)	D1453G	probably damaging	Het
Thoc5	T	C	11: 4,852,156 (GRCm39)	L104S	probably damaging	Het
Tln2	T	G	9: 67,302,755 (GRCm39)	Y72S	probably damaging	Het
Tmem98	A	G	11: 80,705,137 (GRCm39)	E75G	probably damaging	Het
Tox3	A	G	8: 90,975,560 (GRCm39)	L357P	probably damaging	Het
Ubr4	T	C	4: 139,197,603 (GRCm39)	V4492A	unknown	Het
Ulk4	A	G	9: 121,095,578 (GRCm39)		probably null	Het
Ush2a	A	G	1: 188,175,603 (GRCm39)	T1234A	probably benign	Het
Usp53	G	A	3: 122,742,887 (GRCm39)	T683I	probably damaging	Het
Vcan	T	A	13: 89,837,442 (GRCm39)	I2701F	probably damaging	Het
Vmn2r72	G	A	7: 85,399,834 (GRCm39)	A405V	probably damaging	Het
Vmn2r96	A	T	17: 18,806,663 (GRCm39)	T537S	possibly damaging	Het
Vstm2a	G	T	11: 16,213,040 (GRCm39)	A142S	probably damaging	Het
Zbtb41	A	G	1: 139,374,895 (GRCm39)	D785G	probably benign	Het
Zfp397	A	T	18: 24,090,129 (GRCm39)	Q144H	probably benign	Het
Zfp518a	A	T	19: 40,904,249 (GRCm39)	T1393S	possibly 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
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
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
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'- TGAGGGACATTAACGACAACCC -3'
(R):5'- CCCATTTGGAACGTTTTCTGG -3'

Sequencing Primer
(F):5'- TTAACGACAACCCTCCCAGG -3'
(R):5'- GGAGCATTATCATTGGCATCCAGC -3'

Posted On

2019-11-26