Mutagenetix > Incidental Mutation

Incidental Mutation 'R5223:Pcdha2'

402470

Institutional Source

Beutler Lab

Gene Symbol

Pcdha2

Ensembl Gene

ENSMUSG00000104148

Gene Name

protocadherin alpha 2

Synonyms

MMRRC Submission

042796-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.191) question?

Stock #

R5223 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

37072258-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 37073844 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 492 (Y492H)

Ref Sequence

ENSEMBL: ENSMUSP00000141355 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115662] [ENSMUST00000193839] [ENSMUST00000195590]

AlphaFold

Q91Y17

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 damaging
Transcript: ENSMUST00000115662
AA Change: Y492H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148
AA Change: Y492H

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: 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 damaging
Transcript: ENSMUST00000195590
AA Change: Y492H

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148
AA Change: Y492H

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: 99.2%
3x: 98.4%
10x: 96.6%
20x: 93.2%

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: 70 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aatk	C	T	11: 119,904,278 (GRCm39)	V273M	possibly damaging	Het
Acin1	CCGC	CC	14: 54,880,398 (GRCm39)		probably null	Het
Acvr1b	T	A	15: 101,091,857 (GRCm39)	C46S	probably damaging	Het
Ahi1	A	T	10: 20,846,818 (GRCm39)	H416L	possibly damaging	Het
Aspm	T	A	1: 139,406,072 (GRCm39)	L1653Q	probably damaging	Het
Cacna1a	G	A	8: 85,313,824 (GRCm39)	V1533M	possibly damaging	Het
Ccdc33	C	T	9: 57,940,267 (GRCm39)	E502K	possibly damaging	Het
Ctnnd1	C	T	2: 84,447,133 (GRCm39)	V371M	probably damaging	Het
Cyp2a12	A	T	7: 26,735,888 (GRCm39)		probably null	Het
Dnai4	T	A	4: 102,906,600 (GRCm39)	S738C	possibly damaging	Het
Ep400	A	G	5: 110,816,496 (GRCm39)	V2675A	probably damaging	Het
Foxh1	T	A	15: 76,552,929 (GRCm39)		probably null	Het
Gad1-ps	G	A	10: 99,281,009 (GRCm39)		noncoding transcript	Het
Gpnmb	C	T	6: 49,033,139 (GRCm39)	T539M	probably benign	Het
Hdac1-ps	A	G	17: 78,799,867 (GRCm39)	E286G	probably benign	Het
Hspa9	A	G	18: 35,085,724 (GRCm39)		probably null	Het
Hspg2	T	C	4: 137,271,225 (GRCm39)	L2454P	probably damaging	Het
Ift140	T	A	17: 25,254,786 (GRCm39)	I422N	probably benign	Het
Igkv6-32	T	C	6: 70,051,207 (GRCm39)	S50G	probably benign	Het
Il23r	T	A	6: 67,463,154 (GRCm39)	Y113F	probably benign	Het
Kcnt1	A	G	2: 25,793,434 (GRCm39)	D636G	probably benign	Het
Klhl41	G	A	2: 69,510,171 (GRCm39)	W569*	probably null	Het
Klra4	T	A	6: 130,039,110 (GRCm39)	D94V	probably damaging	Het
Lca5	T	A	9: 83,280,666 (GRCm39)	H378L	probably benign	Het
Lhx8	T	A	3: 154,027,281 (GRCm39)	T254S	probably damaging	Het
Lrch3	C	T	16: 32,734,767 (GRCm39)	R86W	probably damaging	Het
Lrp2	T	A	2: 69,354,397 (GRCm39)	N477I	probably damaging	Het
Man2a1	T	A	17: 65,019,266 (GRCm39)	I710K	probably benign	Het
Ncor1	A	T	11: 62,229,826 (GRCm39)	Y881N	probably damaging	Het
Nhsl1	T	A	10: 18,402,074 (GRCm39)	V1100E	probably damaging	Het
Oprk1	T	C	1: 5,659,519 (GRCm39)	V83A	probably benign	Het
Or4p8	T	C	2: 88,727,678 (GRCm39)	T88A	probably benign	Het
Or5p62	A	G	7: 107,771,915 (GRCm39)	V12A	probably benign	Het
Or7g35	T	C	9: 19,496,322 (GRCm39)	V163A	probably benign	Het
Pacs1	C	T	19: 5,195,169 (GRCm39)	V472I	probably benign	Het
Pard3b	T	C	1: 62,383,272 (GRCm39)	Y789H	probably damaging	Het
Pcnt	T	C	10: 76,216,106 (GRCm39)	N2261D	probably damaging	Het
Pex5l	A	T	3: 33,012,945 (GRCm39)	S15T	probably damaging	Het
Plekhg4	A	G	8: 106,105,581 (GRCm39)	N682S	probably benign	Het
Poc5	A	T	13: 96,539,463 (GRCm39)	M335L	probably benign	Het
Polr1a	C	T	6: 71,944,891 (GRCm39)	R1316W	possibly damaging	Het
Pp2d1	T	C	17: 53,814,873 (GRCm39)	H617R	probably benign	Het
Pramel24	T	A	4: 143,454,591 (GRCm39)	S296R	probably benign	Het
Prpsap1	T	C	11: 116,378,974 (GRCm39)	K65E	probably benign	Het
Ptgfrn	T	C	3: 100,952,909 (GRCm39)	E775G	probably benign	Het
Ptprc	T	A	1: 138,045,600 (GRCm39)	I87F	probably benign	Het
Rbbp8	C	A	18: 11,854,747 (GRCm39)	A324E	probably benign	Het
Rfx6	G	T	10: 51,554,092 (GRCm39)	G63*	probably null	Het
Rpl37a	T	C	1: 72,751,308 (GRCm39)	M47T	probably benign	Het
Samm50	T	G	15: 84,084,831 (GRCm39)	N187K	probably benign	Het
Skic2	A	G	17: 35,064,142 (GRCm39)		probably null	Het
Slamf9	T	C	1: 172,303,799 (GRCm39)	I48T	possibly damaging	Het
Slc2a12	A	G	10: 22,577,931 (GRCm39)	K576E	probably damaging	Het
Slc4a10	G	A	2: 62,083,710 (GRCm39)	G388S	probably damaging	Het
Smtn	G	T	11: 3,479,530 (GRCm39)	N512K	probably benign	Het
Sntb1	C	G	15: 55,506,191 (GRCm39)	G461R	probably damaging	Het
Sspo	A	G	6: 48,455,258 (GRCm39)	Y3040C	probably damaging	Het
Stat1	T	A	1: 52,183,401 (GRCm39)	V389E	probably damaging	Het
Sult5a1	A	T	8: 123,872,161 (GRCm39)	M227K	probably damaging	Het
Thsd4	T	C	9: 59,964,325 (GRCm39)	D389G	probably damaging	Het
Tnxb	T	C	17: 34,923,052 (GRCm39)	V2545A	possibly damaging	Het
Tpo	T	A	12: 30,142,589 (GRCm39)	I712F	probably damaging	Het
Trim62	T	C	4: 128,803,204 (GRCm39)	V418A	probably damaging	Het
Uqcrc1	C	A	9: 108,771,224 (GRCm39)	H95N	probably damaging	Het
Vmn2r114	ATTT	ATT	17: 23,509,906 (GRCm39)		probably null	Het
Vmn2r66	T	C	7: 84,657,093 (GRCm39)	D104G	probably benign	Het
Wdr26	T	C	1: 181,015,251 (GRCm39)	I371V	probably benign	Het
Zfp273	T	G	13: 67,974,298 (GRCm39)	C475W	probably damaging	Het
Zfp738	G	T	13: 67,821,182 (GRCm39)	T55K	probably damaging	Het
Zmym2	A	G	14: 57,183,971 (GRCm39)	I978V	probably benign	Het

Other mutations in Pcdha2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL03052:Pcdha2	UTSW	18	37,074,670 (GRCm39)	missense	probably damaging	1.00
R3157:Pcdha2	UTSW	18	37,073,145 (GRCm39)	missense	probably damaging	1.00
R3159:Pcdha2	UTSW	18	37,074,250 (GRCm39)	missense	probably damaging	1.00
R3806:Pcdha2	UTSW	18	37,074,744 (GRCm39)	nonsense	probably null
R3806:Pcdha2	UTSW	18	37,072,582 (GRCm39)	missense	probably benign	0.02
R3815:Pcdha2	UTSW	18	37,074,748 (GRCm39)	missense	probably benign
R3816:Pcdha2	UTSW	18	37,074,748 (GRCm39)	missense	probably benign
R3937:Pcdha2	UTSW	18	37,074,376 (GRCm39)	missense	probably benign	0.42
R3970:Pcdha2	UTSW	18	37,073,750 (GRCm39)	nonsense	probably null
R4058:Pcdha2	UTSW	18	37,072,935 (GRCm39)	missense	probably benign	0.07
R4059:Pcdha2	UTSW	18	37,072,935 (GRCm39)	missense	probably benign	0.07
R4179:Pcdha2	UTSW	18	37,074,529 (GRCm39)	missense	probably damaging	1.00
R4457:Pcdha2	UTSW	18	37,073,599 (GRCm39)	missense	probably damaging	1.00
R4724:Pcdha2	UTSW	18	37,073,568 (GRCm39)	missense	possibly damaging	0.88
R4812:Pcdha2	UTSW	18	37,072,861 (GRCm39)	missense	probably benign
R4884:Pcdha2	UTSW	18	37,073,953 (GRCm39)	missense	probably damaging	1.00
R5130:Pcdha2	UTSW	18	37,073,722 (GRCm39)	missense	probably damaging	1.00
R5442:Pcdha2	UTSW	18	37,072,915 (GRCm39)	missense	probably benign	0.14
R5460:Pcdha2	UTSW	18	37,072,474 (GRCm39)	missense	probably damaging	1.00
R5493:Pcdha2	UTSW	18	37,072,562 (GRCm39)	missense	probably damaging	0.98
R5946:Pcdha2	UTSW	18	37,074,159 (GRCm39)	missense	probably damaging	0.96
R6054:Pcdha2	UTSW	18	37,073,857 (GRCm39)	missense	probably damaging	1.00
R7378:Pcdha2	UTSW	18	37,072,438 (GRCm39)	missense	possibly damaging	0.88
R7465:Pcdha2	UTSW	18	37,073,383 (GRCm39)	missense	probably damaging	1.00
R7542:Pcdha2	UTSW	18	37,073,142 (GRCm39)	missense	probably damaging	0.99
R7774:Pcdha2	UTSW	18	37,074,579 (GRCm39)	missense	probably benign
R7953:Pcdha2	UTSW	18	37,072,579 (GRCm39)	missense	probably benign	0.00
R8043:Pcdha2	UTSW	18	37,072,579 (GRCm39)	missense	probably benign	0.00
R8048:Pcdha2	UTSW	18	37,072,513 (GRCm39)	missense	probably damaging	1.00
R8371:Pcdha2	UTSW	18	37,073,316 (GRCm39)	missense	possibly damaging	0.84
R8414:Pcdha2	UTSW	18	37,074,619 (GRCm39)	missense	probably damaging	1.00
R8472:Pcdha2	UTSW	18	37,074,325 (GRCm39)	missense	probably damaging	1.00
R8998:Pcdha2	UTSW	18	37,073,428 (GRCm39)	missense	possibly damaging	0.92
R8999:Pcdha2	UTSW	18	37,073,428 (GRCm39)	missense	possibly damaging	0.92
R9197:Pcdha2	UTSW	18	37,072,879 (GRCm39)	missense	probably damaging	1.00
R9462:Pcdha2	UTSW	18	37,073,546 (GRCm39)	missense	probably benign	0.07
R9781:Pcdha2	UTSW	18	37,074,102 (GRCm39)	missense	probably benign	0.09
Z1088:Pcdha2	UTSW	18	37,074,174 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- CACAGCTGACTATAAGGTAATGGTG -3'
(R):5'- AGAGTCACATTGCTGCCCAG -3'

Sequencing Primer
(F):5'- TGGTGACAGCGCGGGATG -3'
(R):5'- CAGGGCAGGCACACCAG -3'

Posted On

2016-07-22