Mutagenetix > Incidental Mutation

Incidental Mutation 'R5782:Pcdhga3'

447836

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga3

Ensembl Gene

ENSMUSG00000104346

Gene Name

protocadherin gamma subfamily A, 3

Synonyms

MMRRC Submission

043379-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.121) question?

Stock #

R5782 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

37807388-37974926 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 37809353 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Phenylalanine at position 602 (S602F)

Ref Sequence

ENSEMBL: ENSMUSP00000073150 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000192931] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194544]

AlphaFold

Q91XY5

Predicted Effect

possibly damaging
Transcript: ENSMUST00000073447
AA Change: S602F

PolyPhen 2 Score 0.910 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346
AA Change: S602F

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 benign
Transcript: ENSMUST00000192931

SMART Domains

Protein: ENSMUSP00000141348
Gene: ENSMUSG00000103037

Domain	Start	End	E-Value	Type
CA	36	119	8e-3	SMART
CA	143	228	1.34e-20	SMART
CA	252	333	1.52e-24	SMART
CA	357	438	9.22e-24	SMART
CA	462	548	1.24e-24	SMART
CA	579	660	1.3e-9	SMART
transmembrane domain	679	701	N/A	INTRINSIC
low complexity region	899	918	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193869

SMART Domains

Protein: ENSMUSP00000141482
Gene: ENSMUSG00000103332

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

noncoding transcript
Transcript: ENSMUST00000195624

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.5%
20x: 95.8%

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 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
Actl9	A	T	17: 33,652,735 (GRCm39)	Q265L	probably benign	Het
Adamtsl3	T	A	7: 82,189,494 (GRCm39)		probably null	Het
Agt	A	T	8: 125,283,870 (GRCm39)		probably null	Het
Ankrd11	A	G	8: 123,626,756 (GRCm39)	L142P	probably damaging	Het
Arhgef19	C	A	4: 140,983,623 (GRCm39)	Q719K	probably damaging	Het
Armh3	A	G	19: 45,874,466 (GRCm39)	V569A	probably benign	Het
Atrnl1	G	T	19: 57,741,718 (GRCm39)	W1159L	possibly damaging	Het
Atxn2	T	C	5: 121,935,373 (GRCm39)	Y325H	probably damaging	Het
Brwd1	A	T	16: 95,844,243 (GRCm39)	Y770*	probably null	Het
Cdc20	T	C	4: 118,290,239 (GRCm39)	E474G	probably benign	Het
Cdk5rap3	A	G	11: 96,802,412 (GRCm39)	L254P	probably benign	Het
Cep83	A	T	10: 94,584,894 (GRCm39)	N333I	probably damaging	Het
Cox4i2	A	C	2: 152,606,731 (GRCm39)	D150A	probably damaging	Het
Cse1l	A	G	2: 166,770,921 (GRCm39)	I314M	probably damaging	Het
Cuedc1	A	G	11: 88,060,858 (GRCm39)	Y67C	probably damaging	Het
Cyp2j9	C	T	4: 96,462,142 (GRCm39)	V380I	probably benign	Het
Fancd2	A	G	6: 113,525,833 (GRCm39)	N302S	probably benign	Het
Foxa1	T	A	12: 57,589,302 (GRCm39)	H306L	probably benign	Het
Gse1	T	C	8: 121,293,260 (GRCm39)	S204P	probably damaging	Het
Hspa13	C	A	16: 75,554,985 (GRCm39)	R367L	probably damaging	Het
Kcnk2	T	G	1: 188,988,776 (GRCm39)	D267A	probably damaging	Het
Kctd18	A	G	1: 57,998,396 (GRCm39)	Y68H	probably damaging	Het
Khdc4	T	G	3: 88,618,985 (GRCm39)	V563G	probably damaging	Het
Klf7	C	T	1: 64,081,570 (GRCm39)	E253K	possibly damaging	Het
Lcn12	A	T	2: 25,383,769 (GRCm39)	F34I	probably damaging	Het
Lrrk2	A	T	15: 91,586,386 (GRCm39)	R401W	probably damaging	Het
Lzts1	A	T	8: 69,593,350 (GRCm39)	S86T	probably benign	Het
Mtres1	T	C	10: 43,408,899 (GRCm39)	I81M	probably benign	Het
Mtus1	T	A	8: 41,535,764 (GRCm39)	I651F	probably damaging	Het
Myl2	T	A	5: 122,242,933 (GRCm39)	F106L	probably damaging	Het
Neb	T	A	2: 52,154,059 (GRCm39)	K2351*	probably null	Het
Or14c45	T	A	7: 86,176,421 (GRCm39)	I152N	probably damaging	Het
Or52e5	T	C	7: 104,718,956 (GRCm39)	I94T	probably damaging	Het
Otogl	G	A	10: 107,612,978 (GRCm39)		silent	Het
Parg	A	T	14: 31,996,862 (GRCm39)	R318*	probably null	Het
Pcnx2	A	G	8: 126,480,223 (GRCm39)	V2028A	probably damaging	Het
Pkhd1	T	C	1: 20,128,824 (GRCm39)	T3960A	probably benign	Het
Psen1	T	A	12: 83,759,233 (GRCm39)	H81Q	possibly damaging	Het
Psma6	A	G	12: 55,457,041 (GRCm39)	N109S	possibly damaging	Het
Ptpro	A	T	6: 137,376,496 (GRCm39)	I659F	possibly damaging	Het
Rap1gds1	C	G	3: 138,664,840 (GRCm39)	E288D	possibly damaging	Het
Reln	C	T	5: 22,223,054 (GRCm39)	R993K	probably benign	Het
Saxo1	T	A	4: 86,364,044 (GRCm39)	L146F	probably damaging	Het
Six4	A	G	12: 73,150,832 (GRCm39)	V571A	probably benign	Het
Slc2a10	C	A	2: 165,356,758 (GRCm39)	Y139*	probably null	Het
Slc34a1	A	G	13: 55,550,501 (GRCm39)	I66V	possibly damaging	Het
Slfn8	G	T	11: 82,907,867 (GRCm39)	N46K	probably damaging	Het
Smc6	G	C	12: 11,340,835 (GRCm39)	A496P	probably damaging	Het
Stk31	T	G	6: 49,446,070 (GRCm39)	N902K	probably benign	Het
Stk36	T	A	1: 74,644,584 (GRCm39)	Y114N	possibly damaging	Het
Sult2b1	C	T	7: 45,380,770 (GRCm39)	V271M	probably damaging	Het
Tenm4	A	G	7: 96,542,246 (GRCm39)	I1920V	probably benign	Het
Trbc2	A	G	6: 41,523,871 (GRCm39)		probably benign	Het
Trpc2	A	G	7: 101,733,186 (GRCm39)	D419G	possibly damaging	Het
Trpm7	T	C	2: 126,639,634 (GRCm39)	N1654S	probably benign	Het
Tsku	A	T	7: 98,002,057 (GRCm39)	D91E	probably damaging	Het
Ttn	T	A	2: 76,606,355 (GRCm39)	R18151S	probably damaging	Het
Tyr	C	T	7: 87,142,224 (GRCm39)	C112Y	probably damaging	Het
Ubash3a	G	A	17: 31,454,477 (GRCm39)	G435S	probably benign	Het
Vav1	T	C	17: 57,603,001 (GRCm39)	I51T	probably damaging	Het
Vmn2r61	T	A	7: 41,949,253 (GRCm39)	C558S	probably damaging	Het
Zan	C	T	5: 137,418,269 (GRCm39)	C2943Y	unknown	Het
Zfp1002	T	C	2: 150,097,438 (GRCm39)	E25G	probably benign	Het
Zfp267	T	C	3: 36,219,128 (GRCm39)	S384P	possibly damaging	Het
Zfp318	TGAAGAAGAAGAAGAAGAAGAAGAAGAAG	TGAAGAAGAAGAAGAAGAAGAAG	17: 46,723,440 (GRCm39)		probably benign	Het
Zfp575	C	A	7: 24,285,027 (GRCm39)	G205C	possibly damaging	Het
Zfp740	G	T	15: 102,116,801 (GRCm39)		probably benign	Het
Zzz3	A	G	3: 152,133,737 (GRCm39)	E265G	possibly damaging	Het

Other mutations in Pcdhga3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00934:Pcdhga3	APN	18	37,808,486 (GRCm39)	missense	possibly damaging	0.92
R2863:Pcdhga3	UTSW	18	37,807,643 (GRCm39)	missense	probably damaging	0.99
R4446:Pcdhga3	UTSW	18	37,808,938 (GRCm39)	missense	probably damaging	0.99
R4581:Pcdhga3	UTSW	18	37,809,934 (GRCm39)	missense	probably benign	0.00
R4747:Pcdhga3	UTSW	18	37,809,799 (GRCm39)	missense	probably benign	0.29
R4964:Pcdhga3	UTSW	18	37,809,154 (GRCm39)	missense	probably benign	0.05
R5165:Pcdhga3	UTSW	18	37,808,723 (GRCm39)	missense	possibly damaging	0.60
R5210:Pcdhga3	UTSW	18	37,808,963 (GRCm39)	missense	probably benign	0.03
R5370:Pcdhga3	UTSW	18	37,808,343 (GRCm39)	missense	probably damaging	1.00
R5402:Pcdhga3	UTSW	18	37,808,747 (GRCm39)	missense	probably benign	0.33
R5610:Pcdhga3	UTSW	18	37,808,276 (GRCm39)	missense	possibly damaging	0.83
R5889:Pcdhga3	UTSW	18	37,809,662 (GRCm39)	missense	probably damaging	1.00
R6058:Pcdhga3	UTSW	18	37,808,141 (GRCm39)	missense	probably damaging	1.00
R6127:Pcdhga3	UTSW	18	37,807,757 (GRCm39)	missense	probably damaging	0.98
R6307:Pcdhga3	UTSW	18	37,809,674 (GRCm39)	unclassified	probably benign
R6893:Pcdhga3	UTSW	18	37,809,598 (GRCm39)	missense	probably benign	0.37
R7013:Pcdhga3	UTSW	18	37,808,674 (GRCm39)	missense	probably damaging	1.00
R7174:Pcdhga3	UTSW	18	37,808,980 (GRCm39)	missense	probably benign	0.02
R7448:Pcdhga3	UTSW	18	37,808,917 (GRCm39)	missense	possibly damaging	0.94
R7492:Pcdhga3	UTSW	18	37,809,178 (GRCm39)	missense	probably benign	0.01
R7509:Pcdhga3	UTSW	18	37,808,910 (GRCm39)	nonsense	probably null
R7914:Pcdhga3	UTSW	18	37,808,013 (GRCm39)	missense	probably benign	0.00
R7984:Pcdhga3	UTSW	18	37,809,549 (GRCm39)	missense	probably benign	0.00
R8782:Pcdhga3	UTSW	18	37,807,865 (GRCm39)	missense	probably damaging	1.00
R9157:Pcdhga3	UTSW	18	37,809,229 (GRCm39)	missense	probably benign	0.40
R9169:Pcdhga3	UTSW	18	37,809,088 (GRCm39)	missense	probably damaging	1.00
R9436:Pcdhga3	UTSW	18	37,808,144 (GRCm39)	missense	probably damaging	1.00
R9437:Pcdhga3	UTSW	18	37,808,144 (GRCm39)	missense	probably damaging	1.00
R9588:Pcdhga3	UTSW	18	37,808,564 (GRCm39)	missense	probably damaging	1.00
R9767:Pcdhga3	UTSW	18	37,808,096 (GRCm39)	missense	probably benign	0.00
R9778:Pcdhga3	UTSW	18	37,807,786 (GRCm39)	missense	probably benign	0.42
Z1177:Pcdhga3	UTSW	18	37,809,674 (GRCm39)	unclassified	probably benign

Predicted Primers

PCR Primer
(F):5'- CACTGAACCTATTTGTGCTGG -3'
(R):5'- CAGGGGTATGGATGCTTTCC -3'

Sequencing Primer
(F):5'- CCTATTTGTGCTGGACCAGAATGAC -3'
(R):5'- ATGTCAGGAATGCTGTCAGCC -3'

Posted On

2016-12-15