Mutagenetix > Incidental Mutation

Incidental Mutation 'R6362:Pcdhga2'

512558

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga2

Ensembl Gene

ENSMUSG00000103332

Gene Name

protocadherin gamma subfamily A, 2

Synonyms

MMRRC Submission

044512-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.090) question?

Stock #

R6362 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

37802006-37974923 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37803958 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Asparagine to Aspartic acid at position 601 (N601D)

Ref Sequence

ENSEMBL: ENSMUSP00000141482 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194544]

AlphaFold

Q91XY6

Predicted Effect

probably benign
Transcript: ENSMUST00000073447

SMART Domains

Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CA	42	128	2.15e-2	SMART
CA	152	237	4.8e-13	SMART
CA	261	342	9.36e-25	SMART
CA	366	447	6.62e-25	SMART
CA	471	557	6.72e-26	SMART
CA	588	666	2.15e-15	SMART
Pfam:Cadherin_C_2	685	768	4.8e-24	PFAM
Pfam:Cadherin_tail	805	928	8.1e-38	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115661

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458

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 damaging
Transcript: ENSMUST00000193869
AA Change: N601D

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

SMART Domains

Protein: ENSMUSP00000141482
Gene: ENSMUSG00000103332
AA Change: N601D

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	45	131	1.64e-2	SMART
CA	155	240	6.42e-23	SMART
CA	264	345	1.76e-20	SMART
CA	369	450	2.27e-23	SMART
CA	474	560	1.5e-23	SMART
CA	591	669	1.17e-16	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	912	931	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000194190

SMART Domains

Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	31	131	3.16e-2	SMART
CA	155	240	5.39e-16	SMART
CA	264	345	6.72e-26	SMART
CA	369	450	1.32e-24	SMART
CA	474	560	4.17e-22	SMART
CA	591	669	4.48e-13	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	912	931	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194544

SMART Domains

Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

Domain	Start	End	E-Value	Type
Blast:CA	18	66	5e-20	BLAST

Meta Mutation Damage Score

0.8984

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 96.0%

Validation Efficiency

99% (78/79)

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 gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Aldh5a1	T	G	13: 25,102,533 (GRCm39)	D310A	probably benign	Het
Als2cl	T	A	9: 110,724,514 (GRCm39)		probably null	Het
Amacr	C	A	15: 10,984,891 (GRCm39)	R170S	probably damaging	Het
Brwd1	C	T	16: 95,803,507 (GRCm39)	R2221Q	probably damaging	Het
Cacna1g	A	T	11: 94,330,533 (GRCm39)		probably null	Het
Cd3d	G	A	9: 44,897,589 (GRCm39)	D157N	probably damaging	Het
Cep131	T	C	11: 119,955,516 (GRCm39)	D1043G	probably damaging	Het
Cimip1	T	G	2: 173,369,967 (GRCm39)		probably null	Het
Cit	A	G	5: 116,024,735 (GRCm39)	D326G	probably benign	Het
Col16a1	G	C	4: 129,959,983 (GRCm39)	G370R	unknown	Het
Col6a3	T	A	1: 90,738,285 (GRCm39)	Y1078F	probably damaging	Het
Colgalt2	A	C	1: 152,347,549 (GRCm39)	Y161S	probably damaging	Het
Cyp2j13	A	G	4: 95,959,932 (GRCm39)	Y75H	probably damaging	Het
Daxx	G	A	17: 34,130,338 (GRCm39)	V118I	probably damaging	Het
Dennd5a	G	T	7: 109,533,472 (GRCm39)	C75*	probably null	Het
Diaph3	A	G	14: 87,009,566 (GRCm39)	L1071P	probably damaging	Het
Disp3	A	G	4: 148,338,765 (GRCm39)	L802P	possibly damaging	Het
Dmc1	A	G	15: 79,473,024 (GRCm39)	V141A	probably benign	Het
Dsc2	A	T	18: 20,168,520 (GRCm39)	Y45*	probably null	Het
Dspp	A	G	5: 104,323,900 (GRCm39)	I348V	probably benign	Het
Epb42	C	A	2: 120,856,260 (GRCm39)	C428F	possibly damaging	Het
Fam227a	G	T	15: 79,527,551 (GRCm39)	P100Q	possibly damaging	Het
Fer1l4	C	T	2: 155,890,170 (GRCm39)	V252I	probably benign	Het
Fhod1	C	A	8: 106,058,273 (GRCm39)		probably null	Het
Fhod3	G	T	18: 24,887,312 (GRCm39)	A68S	probably benign	Het
Gatm	T	C	2: 122,428,677 (GRCm39)	D328G	probably benign	Het
Gm6401	G	T	14: 41,789,727 (GRCm39)	H44N	probably benign	Het
Gpat2	G	C	2: 127,273,838 (GRCm39)	G294R	possibly damaging	Het
Gpr84	G	A	15: 103,216,937 (GRCm39)	A380V	probably damaging	Het
Herc1	G	T	9: 66,379,190 (GRCm39)	W3492L	probably damaging	Het
Hjurp	A	T	1: 88,202,772 (GRCm39)	Y71N	possibly damaging	Het
Jag2	T	A	12: 112,883,742 (GRCm39)	K246N	probably damaging	Het
Klhl32	T	C	4: 24,629,195 (GRCm39)	D524G	probably null	Het
Lax1	A	G	1: 133,608,334 (GRCm39)	S136P	possibly damaging	Het
Lefty1	A	G	1: 180,764,725 (GRCm39)	K217E	probably benign	Het
Lgr5	A	G	10: 115,314,430 (GRCm39)	L169P	probably damaging	Het
Lrrc37	G	C	11: 103,511,478 (GRCm39)	N163K	unknown	Het
Mad1l1	A	T	5: 140,300,810 (GRCm39)	S29T	possibly damaging	Het
Man1a	T	C	10: 53,950,891 (GRCm39)	H77R	probably benign	Het
Met	C	T	6: 17,558,732 (GRCm39)	S1120F	probably damaging	Het
Mfsd4b2	A	T	10: 39,797,605 (GRCm39)	I250N	probably damaging	Het
Myod1	A	G	7: 46,026,305 (GRCm39)	H70R	possibly damaging	Het
Neb	T	C	2: 52,102,704 (GRCm39)	N4280S	probably benign	Het
Nudt6	T	C	3: 37,473,638 (GRCm39)	T28A	possibly damaging	Het
Nup85	A	G	11: 115,474,560 (GRCm39)	E628G	probably damaging	Het
Oaz3	A	T	3: 94,342,295 (GRCm39)	D120E	probably damaging	Het
Or2y3	A	T	17: 38,393,620 (GRCm39)	M83K	probably damaging	Het
Or5b102	A	T	19: 13,040,709 (GRCm39)		probably benign	Het
Or5be3	C	T	2: 86,863,633 (GRCm39)	A311T	probably benign	Het
Or5m8	C	A	2: 85,822,285 (GRCm39)	N41K	probably damaging	Het
Or6c1b	A	C	10: 129,272,812 (GRCm39)	I44L	probably damaging	Het
Osbpl8	A	T	10: 111,108,929 (GRCm39)	K404*	probably null	Het
Pld2	T	C	11: 70,445,501 (GRCm39)	Y638H	probably damaging	Het
Pramel27	A	G	4: 143,579,435 (GRCm39)	Y340C	probably damaging	Het
Prickle2	C	G	6: 92,435,596 (GRCm39)	V2L	possibly damaging	Het
Psmd6	G	A	14: 14,116,949 (GRCm38)	R125C	probably benign	Het
Rnaset2b	G	A	17: 7,259,093 (GRCm39)	V24I	probably benign	Het
Rusc2	A	T	4: 43,416,416 (GRCm39)	D574V	probably benign	Het
Scn8a	T	A	15: 100,837,996 (GRCm39)		probably null	Het
Sec11a	T	C	7: 80,572,879 (GRCm39)	E134G	probably benign	Het
Senp5	A	G	16: 31,808,702 (GRCm39)	V157A	probably damaging	Het
Shkbp1	C	T	7: 27,051,120 (GRCm39)		probably null	Het
Slc43a1	T	C	2: 84,690,128 (GRCm39)	L435P	probably damaging	Het
Spn	G	A	7: 126,735,895 (GRCm39)	P204L	possibly damaging	Het
Srr	T	A	11: 74,801,028 (GRCm39)	Q173L	probably damaging	Het
Star	C	G	8: 26,301,835 (GRCm39)	T222S	probably benign	Het
Timm22	T	A	11: 76,301,953 (GRCm39)	Y93N	probably damaging	Het
Tmc4	G	T	7: 3,678,458 (GRCm39)	Q58K	probably benign	Het
Tmem86b	C	T	7: 4,632,835 (GRCm39)	M1I	probably null	Het
Tmtc2	A	T	10: 105,205,831 (GRCm39)	I488N	probably damaging	Het
Tnxb	A	T	17: 34,913,362 (GRCm39)	Y1792F	probably damaging	Het
Tph1	T	A	7: 46,296,867 (GRCm39)	R443W	possibly damaging	Het
Ttyh1	T	A	7: 4,132,323 (GRCm39)	V253E	possibly damaging	Het
Usf3	A	G	16: 44,038,940 (GRCm39)	D1140G	probably benign	Het
Usp10	T	C	8: 120,668,055 (GRCm39)	S118P	probably benign	Het
Vmn2r63	C	T	7: 42,552,721 (GRCm39)	C845Y	probably benign	Het
Vmn2r72	G	T	7: 85,400,382 (GRCm39)	F222L	probably damaging	Het
Zfp654	G	A	16: 64,606,457 (GRCm39)	Q582*	probably null	Het
Zfp791	C	T	8: 85,846,279 (GRCm39)		probably benign	Het
Zfp879	T	A	11: 50,729,302 (GRCm39)	D32V	probably damaging	Het

Other mutations in Pcdhga2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R4132:Pcdhga2	UTSW	18	37,803,107 (GRCm39)	missense	possibly damaging	0.83
R4577:Pcdhga2	UTSW	18	37,802,302 (GRCm39)	missense	possibly damaging	0.78
R4792:Pcdhga2	UTSW	18	37,802,452 (GRCm39)	missense	probably benign	0.02
R4904:Pcdhga2	UTSW	18	37,802,932 (GRCm39)	missense	possibly damaging	0.89
R4982:Pcdhga2	UTSW	18	37,802,476 (GRCm39)	missense	probably benign	0.07
R5230:Pcdhga2	UTSW	18	37,802,795 (GRCm39)	missense	probably benign	0.23
R5502:Pcdhga2	UTSW	18	37,803,605 (GRCm39)	missense	possibly damaging	0.91
R6112:Pcdhga2	UTSW	18	37,802,612 (GRCm39)	missense	probably damaging	0.97
R6344:Pcdhga2	UTSW	18	37,803,815 (GRCm39)	missense	probably benign	0.42
R6835:Pcdhga2	UTSW	18	37,803,842 (GRCm39)	missense	probably damaging	1.00
R6925:Pcdhga2	UTSW	18	37,803,638 (GRCm39)	missense	probably damaging	0.98
R6927:Pcdhga2	UTSW	18	37,803,719 (GRCm39)	missense	probably damaging	1.00
R7153:Pcdhga2	UTSW	18	37,802,261 (GRCm39)	missense	probably damaging	1.00
R7486:Pcdhga2	UTSW	18	37,803,461 (GRCm39)	missense	probably benign	0.01
R7657:Pcdhga2	UTSW	18	37,803,481 (GRCm39)	missense	probably damaging	1.00
R7708:Pcdhga2	UTSW	18	37,804,496 (GRCm39)	missense	possibly damaging	0.93
R7720:Pcdhga2	UTSW	18	37,802,993 (GRCm39)	missense	probably damaging	1.00
R7899:Pcdhga2	UTSW	18	37,803,910 (GRCm39)	missense	probably damaging	1.00
R8416:Pcdhga2	UTSW	18	37,803,178 (GRCm39)	missense	probably damaging	1.00
R8528:Pcdhga2	UTSW	18	37,802,221 (GRCm39)	missense	probably benign	0.01
R8744:Pcdhga2	UTSW	18	37,804,373 (GRCm39)	missense	probably benign	0.17
R9043:Pcdhga2	UTSW	18	37,802,963 (GRCm39)	missense	possibly damaging	0.75
R9189:Pcdhga2	UTSW	18	37,802,795 (GRCm39)	missense	possibly damaging	0.57
R9197:Pcdhga2	UTSW	18	37,804,553 (GRCm39)	missense	probably benign	0.01
R9404:Pcdhga2	UTSW	18	37,803,067 (GRCm39)	missense	probably benign
Z1177:Pcdhga2	UTSW	18	37,803,908 (GRCm39)	missense	probably damaging	0.98

Predicted Primers

PCR Primer
(F):5'- GCAATGTGTCCTTGAGCCTG -3'
(R):5'- TGAATCGTCAGGGTTGGCAG -3'

Sequencing Primer
(F):5'- CCTGTTTTTAGTGGACCAGAACGAC -3'
(R):5'- TCCTGATGCTGCCCAGATCAG -3'

Posted On

2018-04-27