Mutagenetix > Incidental Mutation

Incidental Mutation 'R5493:Pcdha2'

432213

Institutional Source

Beutler Lab

Gene Symbol

Pcdha2

Ensembl Gene

ENSMUSG00000104148

Gene Name

protocadherin alpha 2

Synonyms

MMRRC Submission

043054-MU

Accession Numbers

Essential gene?

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

Stock #

R5493 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

37072258-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 37072562 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Leucine at position 64 (F64L)

Ref Sequence

ENSEMBL: ENSMUSP00000111326 (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: F64L

PolyPhen 2 Score 0.977 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148
AA Change: F64L

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

noncoding transcript
Transcript: ENSMUST00000192440

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: F64L

PolyPhen 2 Score 0.974 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148
AA Change: F64L

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: 98.3%
3x: 97.3%
10x: 95.1%
20x: 90.4%

Validation Efficiency

99% (80/81)

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2510009E07Rik	A	G	16: 21,471,993 (GRCm39)	S236P	possibly damaging	Het
A830018L16Rik	C	T	1: 11,615,431 (GRCm39)	R135C	probably damaging	Het
Agpat3	A	G	10: 78,120,069 (GRCm39)	V155A	possibly damaging	Het
Aldh18a1	C	T	19: 40,539,734 (GRCm39)	R747Q	probably damaging	Het
Aloxe3	A	T	11: 69,019,443 (GRCm39)	R119*	probably null	Het
Asap1	A	G	15: 64,002,000 (GRCm39)	V460A	possibly damaging	Het
Bicral	C	A	17: 47,112,620 (GRCm39)	R860L	possibly damaging	Het
Cd180	T	A	13: 102,842,649 (GRCm39)	I565N	probably benign	Het
Cdk13	T	C	13: 17,978,147 (GRCm39)		probably benign	Het
Cdkn2d	T	C	9: 21,200,303 (GRCm39)	D156G	probably benign	Het
Clrn1	A	G	3: 58,753,837 (GRCm39)	S175P	probably damaging	Het
Coro7	A	G	16: 4,450,351 (GRCm39)	L535S	probably damaging	Het
Cse1l	A	G	2: 166,783,110 (GRCm39)		probably benign	Het
Cyp2a12	T	C	7: 26,728,550 (GRCm39)	L7P	unknown	Het
D130043K22Rik	A	G	13: 25,047,586 (GRCm39)	Y377C	probably damaging	Het
Dctn1	G	T	6: 83,159,546 (GRCm39)	R8L	possibly damaging	Het
Duox2	T	C	2: 122,111,977 (GRCm39)	Q1341R	probably damaging	Het
Eif2b3	A	G	4: 116,943,919 (GRCm39)	D447G	possibly damaging	Het
Eif4a3l1	C	G	6: 136,306,555 (GRCm39)	R339G	probably damaging	Het
Fbxw25	T	C	9: 109,481,984 (GRCm39)	Y234C	probably benign	Het
Gcnt2	A	G	13: 41,107,076 (GRCm39)	N315S	possibly damaging	Het
Gm20730	A	T	6: 43,058,746 (GRCm39)	V22E	possibly damaging	Het
Gm4847	T	A	1: 166,457,890 (GRCm39)	I488F	probably damaging	Het
Gmds	A	T	13: 32,124,488 (GRCm39)	M290K	probably benign	Het
Gtf3c1	T	C	7: 125,269,716 (GRCm39)	N699S	probably damaging	Het
Hk3	A	G	13: 55,158,984 (GRCm39)	V479A	probably damaging	Het
Ifnlr1	G	A	4: 135,432,877 (GRCm39)	V438M	probably benign	Het
Il12rb1	C	A	8: 71,262,483 (GRCm39)	P26T	probably benign	Het
Il4i1	G	T	7: 44,489,477 (GRCm39)	R414L	possibly damaging	Het
Ipo4	T	C	14: 55,868,327 (GRCm39)	N490S	probably benign	Het
Kcnmb2	A	G	3: 32,252,291 (GRCm39)	E164G	probably damaging	Het
Kcns1	G	A	2: 164,009,899 (GRCm39)	L287F	probably benign	Het
Kdm1a	ACC	AC	4: 136,284,732 (GRCm39)		probably null	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Knl1	T	A	2: 118,899,211 (GRCm39)	I304K	probably damaging	Het
Ksr2	G	T	5: 117,846,175 (GRCm39)	V681F	probably damaging	Het
Lypd2	T	C	15: 74,606,127 (GRCm39)	T4A	probably benign	Het
Man1a	A	G	10: 53,950,576 (GRCm39)	V182A	probably benign	Het
Or12j4	A	T	7: 140,046,720 (GRCm39)	D202V	probably damaging	Het
Or13e8	A	G	4: 43,696,225 (GRCm39)	F316S	possibly damaging	Het
Or2w2	A	T	13: 21,758,042 (GRCm39)	C195S	probably damaging	Het
Or51f5	A	T	7: 102,424,315 (GRCm39)	R195W	probably benign	Het
Or56b1b	T	C	7: 108,164,774 (GRCm39)	D76G	probably benign	Het
Pgap3	G	C	11: 98,281,540 (GRCm39)	F168L	possibly damaging	Het
Pip5k1b	T	C	19: 24,416,439 (GRCm39)	N16S	probably benign	Het
Ppip5k1	T	A	2: 121,167,253 (GRCm39)	H41L	probably damaging	Het
Ppp1r9a	A	G	6: 5,159,702 (GRCm39)	R1080G	probably damaging	Het
Qrich2	A	C	11: 116,336,774 (GRCm39)		probably null	Het
Rbl2	C	T	8: 91,842,447 (GRCm39)	P1034L	probably damaging	Het
Rbpjl	GCC	GC	2: 164,256,330 (GRCm39)		probably null	Het
Rin2	A	G	2: 145,702,629 (GRCm39)	S442G	probably damaging	Het
Rtca	C	T	3: 116,293,280 (GRCm39)	R71Q	probably benign	Het
Serpind1	A	T	16: 17,157,902 (GRCm39)	N366I	probably damaging	Het
Shox2	C	G	3: 66,888,796 (GRCm39)	G32R	probably damaging	Het
Sp3	T	A	2: 72,768,466 (GRCm39)	N766Y	probably damaging	Het
Spag7	T	A	11: 70,560,059 (GRCm39)	S17C	probably null	Het
Stk25	A	T	1: 93,563,031 (GRCm39)	F7I	probably benign	Het
Tbx15	G	A	3: 99,259,880 (GRCm39)	G584S	probably benign	Het
Tenm2	T	C	11: 36,755,503 (GRCm39)	D165G	probably benign	Het
Tox2	C	A	2: 163,046,649 (GRCm39)	S42*	probably null	Het
Vmn1r39	A	G	6: 66,781,754 (GRCm39)	V188A	probably damaging	Het
Zbtb5	A	T	4: 44,993,941 (GRCm39)	M481K	probably benign	Het
Zfp26	T	C	9: 20,355,615 (GRCm39)	T56A	possibly damaging	Het
Zfp459	C	A	13: 67,556,498 (GRCm39)	C195F	probably damaging	Het
Zfp703	C	T	8: 27,469,233 (GRCm39)	P299L	probably damaging	Het
Zfp764	A	G	7: 127,004,105 (GRCm39)	I342T	probably benign	Het
Zfp942	T	C	17: 22,151,985 (GRCm39)	N7D	probably null	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
R5223:Pcdha2	UTSW	18	37,073,844 (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
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'- GGACTAGAAGTGATGCCTTCTTTG -3'
(R):5'- CGGGTTGTCGTTAATGTCCC -3'

Sequencing Primer
(F):5'- CTAGAAGTGATGCCTTCTTTGAGAGG -3'
(R):5'- GGTTGTCGTTAATGTCCCTCACC -3'

Posted On

2016-10-05