Mutagenetix > Incidental Mutation

Incidental Mutation 'R6307:Pcdhga3'

509509

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga3

Ensembl Gene

ENSMUSG00000104346

Gene Name

protocadherin gamma subfamily A, 3

Synonyms

MMRRC Submission

044412-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.165) question?

Stock #

R6307 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37807388-37974926 bp(+) (GRCm39)

Type of Mutation

unclassified

DNA Base Change (assembly)

T to A at 37809674 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Ref Sequence

ENSEMBL: ENSMUSP00000141348 (fasta)

Gene Model

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

AlphaFold

Q91XY5

Predicted Effect

probably damaging
Transcript: ENSMUST00000073447
AA Change: L709Q

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

SMART Domains

Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346
AA Change: L709Q

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: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.6%

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: 71 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca7	T	C	10: 79,843,221 (GRCm39)	L1232P	probably damaging	Het
Akap6	A	T	12: 53,188,351 (GRCm39)	I1922F	possibly damaging	Het
Ankdd1a	C	T	9: 65,415,343 (GRCm39)	A227T	possibly damaging	Het
Arpc5	T	C	1: 152,647,206 (GRCm39)	V103A	possibly damaging	Het
Atp9a	C	A	2: 168,510,090 (GRCm39)	V430F	probably benign	Het
Bod1	A	G	11: 31,616,932 (GRCm39)	S110P	probably damaging	Het
Cacna1c	C	A	6: 118,590,914 (GRCm39)	V1453F	probably damaging	Het
Capn8	T	A	1: 182,435,264 (GRCm39)	M414K	probably damaging	Het
Cbl	A	T	9: 44,069,809 (GRCm39)		probably null	Het
Ccdc42	A	T	11: 68,479,106 (GRCm39)	Q98L	probably damaging	Het
Ccn3	T	C	15: 54,611,421 (GRCm39)		probably null	Het
Cd200	C	A	16: 45,217,545 (GRCm39)	V49L	probably benign	Het
Celsr1	A	G	15: 85,812,531 (GRCm39)	S2060P	probably benign	Het
Ces1g	A	T	8: 94,057,820 (GRCm39)	H160Q	possibly damaging	Het
Chrnb2	G	T	3: 89,668,831 (GRCm39)	H161Q	probably damaging	Het
Ctns	G	A	11: 73,082,559 (GRCm39)	T57I	probably benign	Het
Cyp3a25	A	T	5: 145,931,766 (GRCm39)	M114K	possibly damaging	Het
D630003M21Rik	A	G	2: 158,057,871 (GRCm39)	F536L	probably benign	Het
Dcc	C	T	18: 71,943,826 (GRCm39)	R275Q	probably benign	Het
Dmxl2	A	T	9: 54,289,990 (GRCm39)	H2508Q	possibly damaging	Het
Elf5	C	A	2: 103,269,757 (GRCm39)	Q113K	probably damaging	Het
Fam83a	T	G	15: 57,849,507 (GRCm39)	V17G	possibly damaging	Het
Farsa	T	C	8: 85,587,674 (GRCm39)		probably null	Het
Fat2	G	C	11: 55,172,106 (GRCm39)	T2869S	possibly damaging	Het
Fgg	A	T	3: 82,920,283 (GRCm39)	Q354L	probably damaging	Het
Folh1	T	C	7: 86,372,517 (GRCm39)	D679G	probably damaging	Het
Gbp4	T	A	5: 105,270,975 (GRCm39)	R83*	probably null	Het
Gm17482	T	A	6: 115,204,311 (GRCm39)		probably benign	Het
Hmgxb4	T	A	8: 75,749,927 (GRCm39)	V481D	possibly damaging	Het
Ifi207	A	C	1: 173,552,619 (GRCm39)	Y926D	probably damaging	Het
Ikzf5	T	A	7: 130,993,377 (GRCm39)	N264Y	probably damaging	Het
Kat6a	T	A	8: 23,430,384 (GRCm39)	M1913K	unknown	Het
Krt33b	A	T	11: 99,915,694 (GRCm39)	C351S	probably benign	Het
Lrp1	T	C	10: 127,427,944 (GRCm39)	D543G	probably damaging	Het
Lrrfip2	C	T	9: 111,053,021 (GRCm39)	R339W	probably damaging	Het
Mapk3	T	G	7: 126,363,454 (GRCm39)	M276R	probably benign	Het
Mgst1	T	C	6: 138,127,827 (GRCm39)	V137A	probably benign	Het
Muc16	T	C	9: 18,558,884 (GRCm39)	T2470A	unknown	Het
Muc4	C	T	16: 32,575,237 (GRCm39)	S1274F	possibly damaging	Het
Myo5c	A	C	9: 75,180,198 (GRCm39)	K713T	possibly damaging	Het
Myzap	T	C	9: 71,466,146 (GRCm39)	D170G	possibly damaging	Het
Naa50	T	C	16: 43,979,831 (GRCm39)	V113A	probably damaging	Het
Neu3	T	C	7: 99,462,929 (GRCm39)	T265A	probably benign	Het
Nin	T	C	12: 70,061,631 (GRCm39)	T2078A	possibly damaging	Het
Nomo1	G	A	7: 45,683,260 (GRCm39)		probably benign	Het
Nprl3	A	G	11: 32,189,828 (GRCm39)	L273P	probably damaging	Het
Oaf	T	A	9: 43,136,216 (GRCm39)	H120L	possibly damaging	Het
Or10s1	T	C	9: 39,985,824 (GRCm39)	S78P	probably damaging	Het
Or13p4	C	T	4: 118,547,145 (GRCm39)	R168H	probably benign	Het
Or8b36	ATTGCTGTTT	ATTGCTGTTTGCTGTTT	9: 37,937,836 (GRCm39)		probably null	Het
Or8k21	T	C	2: 86,145,468 (GRCm39)	H54R	probably benign	Het
Polq	G	A	16: 36,837,718 (GRCm39)		probably null	Het
Prdm8	C	T	5: 98,333,162 (GRCm39)	P243L	possibly damaging	Het
Prim2	T	C	1: 33,701,373 (GRCm39)	D138G	probably benign	Het
Prl2c5	A	G	13: 13,365,175 (GRCm39)	E107G	probably benign	Het
Prr14l	T	A	5: 32,984,869 (GRCm39)	H1542L	probably damaging	Het
Rab26	T	C	17: 24,749,072 (GRCm39)	E203G	probably damaging	Het
Rtkn2	A	T	10: 67,871,662 (GRCm39)	H350L	possibly damaging	Het
Scara3	T	C	14: 66,175,710 (GRCm39)	D19G	probably benign	Het
Scn3a	A	G	2: 65,302,685 (GRCm39)	S1254P	probably damaging	Het
Sdcbp	A	G	4: 6,385,059 (GRCm39)	M93V	probably benign	Het
Sema6a	C	A	18: 47,382,231 (GRCm39)	R772L	probably damaging	Het
Slc5a7	T	C	17: 54,584,006 (GRCm39)	K428R	probably benign	Het
Sptbn2	G	A	19: 4,774,674 (GRCm39)	G109D	probably damaging	Het
Tmppe	T	C	9: 114,233,812 (GRCm39)	L37P	probably benign	Het
Tuba1a	T	C	15: 98,849,410 (GRCm39)	T56A	probably benign	Het
Tut4	T	A	4: 108,412,817 (GRCm39)	I1506N	probably damaging	Het
Vmn2r111	A	G	17: 22,792,070 (GRCm39)	I62T	probably benign	Het
Vmn2r73	A	G	7: 85,506,828 (GRCm39)	I828T	probably damaging	Het
Vmn2r79	T	A	7: 86,686,976 (GRCm39)	W786R	probably damaging	Het
Zp1	G	A	19: 10,894,084 (GRCm39)	T405M	probably null	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
R5782:Pcdhga3	UTSW	18	37,809,353 (GRCm39)	missense	possibly damaging	0.91
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
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'- ACTGTCACGCTCACCATAGC -3'
(R):5'- TATTATAAGAGGCTCGCTTTTCCCAC -3'

Sequencing Primer
(F):5'- TCACGCTCACCATAGCAGTGG -3'
(R):5'- ACAGCTCTCCTGGCTGATGAG -3'

Posted On

2018-04-02