Mutagenetix > Incidental Mutations

Incidental Mutation 'R5194:Pcdhga4'

400036

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga4

Ensembl Gene

ENSMUSG00000103677

Gene Name

protocadherin gamma subfamily A, 4

Synonyms

MMRRC Submission

042770-MU

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.078) question?

Stock #

R5194 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37685210-37841873 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

A to C at 37687741 bp

Zygosity

Heterozygous

Amino Acid Change

Glutamine to Proline at position 781 (Q781P)

Ref Sequence

ENSEMBL: ENSMUSP00000142140 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000192931] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194418] [ENSMUST00000194544] [ENSMUST00000195112]

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 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

noncoding transcript
Transcript: ENSMUST00000193631

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: ENSMUST00000194418
AA Change: Q781P

PolyPhen 2 Score 0.078 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: Q781P

Domain	Start	End	E-Value	Type
CA	44	130	1.64e-2	SMART
CA	154	239	3.93e-18	SMART
CA	263	344	5.22e-23	SMART
CA	368	449	5.02e-25	SMART
CA	473	559	2.07e-26	SMART
CA	590	668	6.84e-18	SMART
transmembrane domain	690	712	N/A	INTRINSIC
low complexity region	911	930	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: ENSMUST00000195112

SMART Domains

Protein: ENSMUSP00000141449
Gene: ENSMUSG00000102748

Domain	Start	End	E-Value	Type
CA	24	130	8.18e-3	SMART
CA	154	239	1.39e-18	SMART
CA	263	344	7.91e-23	SMART
CA	368	449	2.27e-23	SMART
CA	473	559	1.24e-24	SMART
CA	590	671	1.3e-9	SMART
transmembrane domain	690	712	N/A	INTRINSIC
low complexity region	909	928	N/A	INTRINSIC

Predicted Effect

unknown
Transcript: ENSMUST00000195163
AA Change: Q253P

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000195624

Meta Mutation Damage Score

0.0898

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.3%
20x: 95.5%

Validation Efficiency

98% (59/60)

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: 55 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700122O11Rik	T	C	17: 48,037,250	N82D	probably benign	Het
Acadm	C	T	3: 153,933,118	R206H	possibly damaging	Het
Acly	T	A	11: 100,523,546	Y18F	probably benign	Het
Acnat2	G	T	4: 49,380,452	Q291K	probably benign	Het
Agtpbp1	T	C	13: 59,500,639	I456V	probably benign	Het
Ankrd7	A	G	6: 18,868,077	N114S	possibly damaging	Het
Arfgef1	A	T	1: 10,204,907	L307I	probably benign	Het
Arhgef2	A	T	3: 88,635,649	I383F	probably damaging	Het
Cbs	C	T	17: 31,624,224		probably null	Het
Cep135	T	C	5: 76,615,777	V538A	probably benign	Het
D11Wsu47e	T	C	11: 113,688,828	S350P	possibly damaging	Het
Dennd5a	T	C	7: 109,933,729	E254G	probably damaging	Het
Drc7	T	C	8: 95,061,717	V236A	probably benign	Het
Dtna	C	T	18: 23,590,245	Q169*	probably null	Het
Egfem1	G	A	3: 29,357,196		probably null	Het
Eif2ak3	T	C	6: 70,858,478	S130P	possibly damaging	Het
Ewsr1	T	C	11: 5,082,355	N297S	unknown	Het
F13a1	T	G	13: 36,972,063	D192A	probably damaging	Het
Fam120a	A	G	13: 48,880,935	V1067A	probably benign	Het
Gm13124	A	G	4: 144,555,082	V380A	probably benign	Het
Gm17490	T	C	2: 11,626,251	Y5C	unknown	Het
Gm8587	C	T	12: 88,089,786		noncoding transcript	Het
H2-Ab1	C	T	17: 34,269,378		probably benign	Het
Hoxd12	T	C	2: 74,675,103	L6P	probably damaging	Het
Ifi204	C	T	1: 173,749,344	D564N	possibly damaging	Het
Irak2	T	C	6: 113,690,790	V444A	probably benign	Het
Lgr6	C	T	1: 134,994,010	A199T	probably damaging	Het
Lrba	A	C	3: 86,328,219	N877H	probably damaging	Het
Mylk3	T	C	8: 85,352,866	I388V	probably benign	Het
Myo9b	C	T	8: 71,349,089	A1286V	probably benign	Het
Myt1l	A	C	12: 29,811,648	D143A	unknown	Het
Ngfr	T	C	11: 95,580,982	N63S	probably benign	Het
Olfr1264	T	A	2: 90,021,526	Y180F	probably damaging	Het
Olfr1347	A	G	7: 6,488,520	L118P	probably damaging	Het
Olfr576	A	G	7: 102,965,864	I255V	probably benign	Het
Olfr698	A	T	7: 106,753,219	H56Q	probably benign	Het
Olfr814	C	T	10: 129,874,098	V220I	probably benign	Het
P2rx7	T	C	5: 122,673,795	S390P	probably benign	Het
Phip	G	A	9: 82,908,862	S677F	probably benign	Het
Ptpdc1	C	A	13: 48,586,789	V389F	possibly damaging	Het
Rab2a	T	A	4: 8,604,381	I161N	probably benign	Het
Rnf113a2	T	A	12: 84,417,337	M1K	probably null	Het
Schip1	T	C	3: 68,494,872	V122A	probably benign	Het
Sdr16c5	C	A	4: 4,006,663	A210S	probably benign	Het
Sh3bp1	A	G	15: 78,903,101	K83E	probably damaging	Het
Sipa1l2	T	C	8: 125,439,273	S1541G	possibly damaging	Het
Slc22a21	T	C	11: 53,979,847	Y4C	probably damaging	Het
Smco1	C	T	16: 32,273,774	H88Y	probably damaging	Het
Tll2	T	C	19: 41,095,897	D697G	probably damaging	Het
Trim34a	A	G	7: 104,260,993	N334S	possibly damaging	Het
Ubqln1	A	G	13: 58,199,033	I64T	probably benign	Het
Vstm2b	T	A	7: 40,902,488		probably null	Het
Wdr17	A	G	8: 54,687,604	F238L	probably damaging	Het
Wiz	T	C	17: 32,377,848		probably benign	Het
Zfp407	T	C	18: 84,561,309	S560G	probably benign	Het

Other mutations in Pcdhga4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
PIT1430001:Pcdhga4	UTSW	18	37686214	missense	probably benign	0.00
R3828:Pcdhga4	UTSW	18	37687601	missense	possibly damaging	0.62
R3970:Pcdhga4	UTSW	18	37687601	missense	possibly damaging	0.62
R4080:Pcdhga4	UTSW	18	37685779	missense	probably damaging	1.00
R4356:Pcdhga4	UTSW	18	37687611	missense	probably damaging	1.00
R4834:Pcdhga4	UTSW	18	37685437	missense	probably benign	0.01
R4983:Pcdhga4	UTSW	18	37686519	missense	probably damaging	1.00
R5076:Pcdhga4	UTSW	18	37685595	missense	probably benign	0.43
R5186:Pcdhga4	UTSW	18	37687426	missense	probably benign	0.07
R5326:Pcdhga4	UTSW	18	37686598	missense	probably damaging	0.98
R5333:Pcdhga4	UTSW	18	37685424	missense	probably benign	0.00
R5373:Pcdhga4	UTSW	18	37685596	missense	probably damaging	1.00
R5374:Pcdhga4	UTSW	18	37685596	missense	probably damaging	1.00
R5419:Pcdhga4	UTSW	18	37686745	missense	probably damaging	1.00
R5542:Pcdhga4	UTSW	18	37686598	missense	probably damaging	0.98
R5878:Pcdhga4	UTSW	18	37687686	missense	probably benign	0.03
R5996:Pcdhga4	UTSW	18	37685938	missense	probably benign	0.03
R6056:Pcdhga4	UTSW	18	37686330	missense	probably benign	0.00
R6083:Pcdhga4	UTSW	18	37687425	missense	probably damaging	0.98
R6155:Pcdhga4	UTSW	18	37686493	missense	probably damaging	0.98
R6208:Pcdhga4	UTSW	18	37686709	missense	probably damaging	1.00
R6306:Pcdhga4	UTSW	18	37685913	missense	probably damaging	1.00
R6580:Pcdhga4	UTSW	18	37687317	missense	possibly damaging	0.93
R6936:Pcdhga4	UTSW	18	37687405	missense	possibly damaging	0.84
R7132:Pcdhga4	UTSW	18	37687377	missense	probably damaging	1.00
R7159:Pcdhga4	UTSW	18	37686919	missense	probably damaging	1.00
R7257:Pcdhga4	UTSW	18	37687398	missense	probably damaging	0.99
R7263:Pcdhga4	UTSW	18	37686820	missense	probably benign	0.42
R7825:Pcdhga4	UTSW	18	37687321	missense	probably damaging	1.00
R7882:Pcdhga4	UTSW	18	37686628	missense	probably damaging	1.00
R7916:Pcdhga4	UTSW	18	37685449	missense	probably benign	0.22
R8053:Pcdhga4	UTSW	18	37686255	missense	probably benign	0.07

Predicted Primers

PCR Primer
(F):5'- TGTGCTGCTGATACACAGGC -3'
(R):5'- CAAGGGGCTATTACTAAAGAAATGC -3'

Sequencing Primer
(F):5'- TGCTGATACACAGGCTCCGTC -3'
(R):5'- GAAATGCATATTCTTGACACAACAC -3'

Posted On

2016-07-06