Mutagenetix > Incidental Mutation

Incidental Mutation 'R4904:Pcdhga2'

378074

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga2

Ensembl Gene

ENSMUSG00000103332

Gene Name

protocadherin gamma subfamily A, 2

Synonyms

MMRRC Submission

042507-MU

Accession Numbers

Essential gene?

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

Stock #

R4904 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37802006-37974923 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37802932 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 259 (T259A)

Ref Sequence

ENSEMBL: ENSMUSP00000141482 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194544] [ENSMUST00000194888]

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

possibly damaging
Transcript: ENSMUST00000193869
AA Change: T259A

PolyPhen 2 Score 0.887 (Sensitivity: 0.82; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000141482
Gene: ENSMUSG00000103332
AA Change: T259A

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

Predicted Effect

probably benign
Transcript: ENSMUST00000194888

SMART Domains

Protein: ENSMUSP00000141367
Gene: ENSMUSG00000103144

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	31	131	1.6e-4	SMART
CA	155	240	2.7e-18	SMART
CA	264	345	3.3e-28	SMART
CA	369	450	6.7e-27	SMART
CA	474	560	2e-24	SMART
CA	591	669	2.2e-15	SMART
transmembrane domain	692	714	N/A	INTRINSIC

Meta Mutation Damage Score

0.6968

Coding Region Coverage

1x: 99.0%
3x: 98.2%
10x: 95.9%
20x: 91.1%

Validation Efficiency

94% (82/87)

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: 68 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Adgrb2	T	G	4: 129,906,332 (GRCm39)	I920S	possibly damaging	Het
Afap1l1	A	G	18: 61,871,786 (GRCm39)	I556T	probably benign	Het
Ankfy1	C	A	11: 72,642,931 (GRCm39)	H665N	probably benign	Het
Aqp9	A	C	9: 71,069,685 (GRCm39)		probably benign	Het
Arhgap21	A	G	2: 20,854,872 (GRCm39)	S1497P	probably benign	Het
Armc7	A	G	11: 115,379,800 (GRCm39)	D166G	probably damaging	Het
Arrdc1	C	A	2: 24,816,676 (GRCm39)	V167F	possibly damaging	Het
Col6a3	A	T	1: 90,729,164 (GRCm39)	I1259N	probably damaging	Het
Coq8a	C	T	1: 180,006,168 (GRCm39)	R207Q	probably damaging	Het
Cybb	C	G	X: 9,316,989 (GRCm39)	D246H	probably benign	Het
Dcbld1	C	T	10: 52,196,066 (GRCm39)	Q425*	probably null	Het
Def8	A	G	8: 124,188,219 (GRCm39)	N445D	probably damaging	Het
Dicer1	C	T	12: 104,679,325 (GRCm39)	V551I	probably benign	Het
Dst	A	T	1: 34,208,879 (GRCm39)	T800S	probably damaging	Het
Dtl	A	T	1: 191,300,457 (GRCm39)	C136S	probably damaging	Het
Duox1	T	A	2: 122,151,345 (GRCm39)	Y310N	probably damaging	Het
Duxf1	T	A	10: 58,059,309 (GRCm39)	R482*	probably null	Het
Ebf1	T	C	11: 44,759,996 (GRCm39)	F211S	probably damaging	Het
Gm44501	A	T	17: 40,889,884 (GRCm39)	I133F	possibly damaging	Het
Gm6625	T	C	8: 89,873,379 (GRCm39)		noncoding transcript	Het
Golgb1	A	T	16: 36,713,748 (GRCm39)	D243V	probably damaging	Het
Gprc5c	G	T	11: 114,755,093 (GRCm39)	V257L	possibly damaging	Het
Gtf2a1l	G	A	17: 88,997,471 (GRCm39)		probably null	Het
Herc2	T	C	7: 55,807,234 (GRCm39)	F2471L	probably damaging	Het
Hfe	A	T	13: 23,892,037 (GRCm39)	I109N	probably damaging	Het
Hrg	A	G	16: 22,770,000 (GRCm39)	E43G	probably benign	Het
Hspa1a	T	C	17: 35,189,427 (GRCm39)	D492G	probably damaging	Het
Itgb8	T	C	12: 119,134,606 (GRCm39)	D487G	probably benign	Het
Jag1	A	G	2: 136,929,062 (GRCm39)	V798A	probably damaging	Het
Kcnq5	A	G	1: 21,494,324 (GRCm39)	V501A	probably damaging	Het
Kntc1	T	C	5: 123,916,396 (GRCm39)	V743A	possibly damaging	Het
Ly86	G	T	13: 37,599,496 (GRCm39)	V126F	possibly damaging	Het
Med26	A	T	8: 73,250,691 (GRCm39)	L136H	probably damaging	Het
Mpp3	T	C	11: 101,891,413 (GRCm39)	D575G	probably benign	Het
Myoc	G	A	1: 162,466,994 (GRCm39)	M54I	probably benign	Het
Nlrp1c-ps	A	G	11: 71,133,454 (GRCm39)		noncoding transcript	Het
Or10v9	C	T	19: 11,833,231 (GRCm39)	V29M	possibly damaging	Het
Or51t4	A	G	7: 102,598,272 (GRCm39)	Y190C	probably damaging	Het
Or5v1b	A	G	17: 37,841,522 (GRCm39)	Y218C	probably damaging	Het
Pak5	A	T	2: 135,925,267 (GRCm39)	D678E	probably benign	Het
Pcdhb12	T	C	18: 37,570,909 (GRCm39)	V685A	possibly damaging	Het
Pde6a	A	T	18: 61,398,105 (GRCm39)	M702L	probably benign	Het
Pigq	A	G	17: 26,150,034 (GRCm39)		probably benign	Het
Polrmt	A	G	10: 79,582,385 (GRCm39)	M1T	probably null	Het
Ptch1	A	C	13: 63,670,818 (GRCm39)	I904S	probably damaging	Het
Rflnb	A	T	11: 75,912,964 (GRCm39)	C141*	probably null	Het
Rilpl1	C	A	5: 124,652,807 (GRCm39)		probably null	Het
Rpgrip1	T	C	14: 52,358,544 (GRCm39)	S217P	possibly damaging	Het
Rpgrip1	A	T	14: 52,397,586 (GRCm39)	I1292F	probably damaging	Het
Sema3a	A	C	5: 13,631,066 (GRCm39)	Y534S	probably damaging	Het
Sez6	A	G	11: 77,866,080 (GRCm39)	Y736C	probably damaging	Het
Shank1	G	T	7: 43,983,464 (GRCm39)		probably benign	Het
Slc45a4	G	A	15: 73,458,691 (GRCm39)	S294F	probably benign	Het
Slc9a8	A	G	2: 167,313,316 (GRCm39)	I393V	possibly damaging	Het
Sod1	T	A	16: 90,019,732 (GRCm39)	F46Y	probably damaging	Het
Sult1b1	T	C	5: 87,682,912 (GRCm39)	D11G	probably benign	Het
Syn3	T	G	10: 86,302,950 (GRCm39)	K68N	possibly damaging	Het
Taar8c	C	T	10: 23,977,147 (GRCm39)	V222I	probably benign	Het
Tbx20	T	C	9: 24,670,129 (GRCm39)	K235E	probably damaging	Het
Tcaf3	C	A	6: 42,570,931 (GRCm39)	E274*	probably null	Het
Tll1	A	T	8: 64,523,233 (GRCm39)	M493K	probably benign	Het
Tmem236	T	A	2: 14,200,803 (GRCm39)	S123T	probably benign	Het
Trim33	T	C	3: 103,238,963 (GRCm39)	V647A	possibly damaging	Het
Tspear	T	A	10: 77,705,489 (GRCm39)	Y296N	possibly damaging	Het
Vps13d	T	C	4: 144,882,015 (GRCm39)	K1187E	probably damaging	Het
Xpot	C	T	10: 121,453,083 (GRCm39)	V52I	probably benign	Het
Zdhhc3	A	T	9: 122,929,452 (GRCm39)	V61E	probably damaging	Het
Zfp955a	A	T	17: 33,461,162 (GRCm39)	C323*	probably null	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
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
R6362:Pcdhga2	UTSW	18	37,803,958 (GRCm39)	missense	probably damaging	1.00
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'- GAGGAAGAGGCTGTTCATCATC -3'
(R):5'- CGGTGACAATTACTTTCGTCCTAG -3'

Sequencing Primer
(F):5'- AAGAGGCTGTTCATCATCTGGTTC -3'
(R):5'- ACTTTCGTCCTAGTCAGAAGGC -3'

Posted On

2016-04-15