Mutagenetix > Incidental Mutation

Incidental Mutation 'R7542:Pcdha2'

583981

Institutional Source

Beutler Lab

Gene Symbol

Pcdha2

Ensembl Gene

ENSMUSG00000104148

Gene Name

protocadherin alpha 2

Synonyms

MMRRC Submission

045614-MU

Accession Numbers

Essential gene?

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

Stock #

R7542 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37072258-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 37073142 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Arginine at position 258 (G258R)

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: G258R

PolyPhen 2 Score 0.994 (Sensitivity: 0.69; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148
AA Change: G258R

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: G258R

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148
AA Change: G258R

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: 67 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adam24	A	T	8: 41,133,848 (GRCm39)	T439S	possibly damaging	Het
Akap11	A	T	14: 78,747,732 (GRCm39)	S1552T		Het
Akap6	A	G	12: 53,116,017 (GRCm39)	E1040G	probably damaging	Het
Alms1	A	T	6: 85,606,344 (GRCm39)	T2196S	possibly damaging	Het
Alox12e	T	C	11: 70,212,582 (GRCm39)	Q89R	possibly damaging	Het
AW551984	T	A	9: 39,505,927 (GRCm39)	E423D	possibly damaging	Het
Ccpg1	T	A	9: 72,919,741 (GRCm39)	V452D	probably damaging	Het
Cdk5r1	T	C	11: 80,369,190 (GRCm39)	F286L	probably damaging	Het
Cgref1	A	T	5: 31,090,937 (GRCm39)	N292K	probably damaging	Het
Clgn	A	T	8: 84,122,174 (GRCm39)	S32C	possibly damaging	Het
Csk	C	A	9: 57,536,283 (GRCm39)		probably null	Het
Dchs2	A	G	3: 83,176,591 (GRCm39)	T850A	probably benign	Het
Defb2	T	C	8: 22,333,360 (GRCm39)	V45A	probably benign	Het
Disp2	A	G	2: 118,621,599 (GRCm39)	Q777R	probably damaging	Het
Dll1	C	T	17: 15,590,609 (GRCm39)	C369Y	probably damaging	Het
Dnah7c	A	G	1: 46,823,658 (GRCm39)	I3766V	probably benign	Het
Elapor1	A	T	3: 108,365,543 (GRCm39)		probably benign	Het
Fam53a	A	G	5: 33,764,815 (GRCm39)	M297T	probably damaging	Het
Fat4	A	G	3: 39,035,504 (GRCm39)	D3052G	possibly damaging	Het
Fat4	A	T	3: 39,035,770 (GRCm39)	I3141F	possibly damaging	Het
Fbxw10	T	C	11: 62,741,422 (GRCm39)	V180A	probably benign	Het
Frem2	A	T	3: 53,560,000 (GRCm39)	D1502E	probably damaging	Het
Fsip2	A	T	2: 82,815,196 (GRCm39)	N3643I	possibly damaging	Het
Furin	A	G	7: 80,043,207 (GRCm39)	S335P	probably damaging	Het
Glb1l3	C	A	9: 26,729,491 (GRCm39)	A659S	possibly damaging	Het
Gm8011	A	T	14: 42,288,741 (GRCm39)	R175*	probably null	Het
Gna15	A	G	10: 81,350,136 (GRCm39)	S89P	probably damaging	Het
Grm2	A	T	9: 106,528,368 (GRCm39)	L172Q	probably damaging	Het
Iqcn	A	G	8: 71,161,415 (GRCm39)	T203A	possibly damaging	Het
Kcnc3	A	G	7: 44,245,138 (GRCm39)	D476G	possibly damaging	Het
Kcnh6	A	G	11: 105,905,387 (GRCm39)	T216A	possibly damaging	Het
Kdm2a	G	A	19: 4,383,858 (GRCm39)		probably benign	Het
Lrrc9	T	C	12: 72,553,094 (GRCm39)	I1332T	probably damaging	Het
Maea	T	C	5: 33,529,007 (GRCm39)	C317R	probably damaging	Het
Manba	T	C	3: 135,272,354 (GRCm39)	V707A	probably benign	Het
Mcph1	C	T	8: 18,681,705 (GRCm39)	R281C	probably benign	Het
Med25	A	T	7: 44,541,215 (GRCm39)	D99E	probably damaging	Het
Megf10	C	A	18: 57,322,642 (GRCm39)	D62E	probably benign	Het
Minar1	T	A	9: 89,483,964 (GRCm39)	T478S	probably damaging	Het
Myod1	A	T	7: 46,026,097 (GRCm39)	M1L	probably benign	Het
Nav3	A	T	10: 109,659,394 (GRCm39)	M741K	possibly damaging	Het
Odf2l	A	C	3: 144,859,197 (GRCm39)	K618T	probably damaging	Het
Or4c107	A	T	2: 88,789,119 (GRCm39)	E103V	probably benign	Het
Pcdha3	G	A	18: 37,080,784 (GRCm39)	A509T	possibly damaging	Het
Pde4dip	A	G	3: 97,673,971 (GRCm39)	V315A	possibly damaging	Het
Prim1	T	C	10: 127,853,903 (GRCm39)	V107A	probably damaging	Het
Pxdc1	A	G	13: 34,822,146 (GRCm39)		probably null	Het
Rab7b	C	T	1: 131,639,379 (GRCm39)	H182Y	probably benign	Het
Reln	C	A	5: 22,160,179 (GRCm39)	G2130V	probably damaging	Het
Retreg1	T	A	15: 25,941,296 (GRCm39)	M1K	probably null	Het
Rras	G	A	7: 44,669,766 (GRCm39)	R94Q	probably damaging	Het
Rundc3a	T	A	11: 102,290,871 (GRCm39)	L318Q	probably benign	Het
Scgb2b18	A	T	7: 32,872,747 (GRCm39)		probably null	Het
Setd1b	A	T	5: 123,286,510 (GRCm39)	M519L	unknown	Het
Tep1	G	A	14: 51,099,948 (GRCm39)	Q426*	probably null	Het
Tesk1	G	T	4: 43,445,941 (GRCm39)	M291I	probably benign	Het
Tgs1	A	G	4: 3,595,439 (GRCm39)	D536G	probably benign	Het
Thbs1	C	T	2: 117,951,655 (GRCm39)	T825M	probably damaging	Het
Tmem59l	T	C	8: 70,937,814 (GRCm39)	N189D	possibly damaging	Het
Trim30c	A	T	7: 104,031,425 (GRCm39)	D463E	possibly damaging	Het
Trpc4	A	G	3: 54,223,075 (GRCm39)	Y706C	probably damaging	Het
Ttc13	A	T	8: 125,401,842 (GRCm39)		probably null	Het
Tulp1	T	C	17: 28,582,729 (GRCm39)	K140E	probably benign	Het
Urb2	A	G	8: 124,755,327 (GRCm39)	I345V	probably benign	Het
Vmn2r43	T	C	7: 8,258,488 (GRCm39)	M242V	probably benign	Het
Zcwpw1	T	C	5: 137,817,785 (GRCm39)	V509A	probably benign	Het
Zfp202	T	C	9: 40,122,443 (GRCm39)	C402R	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
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
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
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'- TCTTGTGCTGGGAAAATCTCTG -3'
(R):5'- TCCCTTGTCAGATGCAATGACC -3'

Sequencing Primer
(F):5'- TGTGCTGGGAAAATCTCTGGACAG -3'
(R):5'- GTCAGATGCAATGACCTGGATTTC -3'

Posted On

2019-10-17