Mutagenetix > Incidental Mutations

Incidental Mutation 'R7146:Pcdhga1'

553846

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga1

Ensembl Gene

ENSMUSG00000103144

Gene Name

protocadherin gamma subfamily A, 1

Synonyms

MMRRC Submission

Accession Numbers

Is this an essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7146 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

37661793-37841873 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

C to A at 37662111 bp

Zygosity

Heterozygous

Amino Acid Change

Threonine to Asparagine at position 56 (T56N)

Ref Sequence

ENSEMBL: ENSMUSP00000142062 (fasta)

Gene Model

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

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: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000194190
AA Change: T56N

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144
AA Change: T56N

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
AA Change: T56N

PolyPhen 2 Score 0.041 (Sensitivity: 0.94; Specificity: 0.83)

SMART Domains

Protein: ENSMUSP00000141367
Gene: ENSMUSG00000103144
AA Change: T56N

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

0.0898

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.2%

Validation Efficiency

95% (99/104)

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]
PHENOTYPE: Mice homozygous for a null/reporter allele are viable and fertile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 100 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca14	A	T	7: 120,255,297	I895F	probably benign	Het
Abca16	A	G	7: 120,527,751	N1222D	possibly damaging	Het
Abcc4	A	T	14: 118,615,181	Y499N	probably damaging	Het
Adgrg7	A	C	16: 56,730,242	C702W	probably damaging	Het
Adk	C	A	14: 21,326,614	P27H		Het
Ankrd13a	T	C	5: 114,775,232	S2P	probably damaging	Het
Ano1	T	C	7: 144,655,656	H269R	probably benign	Het
Aox3	T	A	1: 58,158,529		probably null	Het
Asl	G	A	5: 130,024,449		probably benign	Het
Asxl2	A	T	12: 3,457,066	D86V	probably damaging	Het
Ate1	A	T	7: 130,481,778		probably null	Het
Bach2	A	G	4: 32,562,670	D379G	probably damaging	Het
Bdkrb1	T	A	12: 105,604,883	L236Q	probably damaging	Het
Cacna2d3	T	C	14: 29,721,697	Y24C	unknown	Het
Cage1	G	T	13: 38,023,049	N273K	probably benign	Het
Ccdc51	T	A	9: 109,091,780	I245N	probably damaging	Het
Cep152	T	C	2: 125,614,405	I229V	probably benign	Het
Chst4	T	A	8: 110,030,731	S167C	probably damaging	Het
Cntnap4	A	T	8: 112,810,636	Y713F	probably damaging	Het
Cntnap5b	G	A	1: 100,050,794		probably null	Het
Cog8	G	T	8: 107,052,373	T424K	possibly damaging	Het
Cop1	T	G	1: 159,244,352		probably null	Het
Cyp2j6	A	G	4: 96,545,782	I97T	probably damaging	Het
D430041D05Rik	T	C	2: 104,258,353	T131A	probably benign	Het
Dnah17	T	C	11: 118,082,110	D1999G	probably damaging	Het
Dnah8	A	G	17: 30,644,617	D250G	probably benign	Het
Dnah8	T	C	17: 30,769,644	V3196A	possibly damaging	Het
Dscam	A	T	16: 96,829,917	Y299*	probably null	Het
Ephb1	A	G	9: 101,963,958	S774P	probably damaging	Het
Fat1	G	A	8: 44,950,925	V238I	probably benign	Het
Fermt1	C	T	2: 132,934,865	M234I	probably benign	Het
Fmnl2	C	T	2: 53,068,540	S212L		Het
Frem1	T	C	4: 82,922,295	N1798S	possibly damaging	Het
Gabrd	T	A	4: 155,385,406	M449L	probably benign	Het
Gad1	T	C	2: 70,587,362	F302L	probably benign	Het
Gm10800	A	AC	2: 98,667,033		probably null	Het
Gm11639	A	G	11: 104,967,752	N3879S	unknown	Het
Gm11639	A	C	11: 105,022,938	D4594A	probably benign	Het
Gm21886	GGGCCTGCAGACAGTAGGTGCTCACTAGGGCCTGTAAATAGTAGGTGCTCACTGAGGCCTGTAGACAGTAGGTGCTCA	GGGCCTGTAGACAGTAGGTGCTCA	18: 80,089,482		probably benign	Het
Gnb3	C	T	6: 124,836,924		probably null	Het
Gtf3c1	A	T	7: 125,672,821	M642K	possibly damaging	Het
Hps3	A	T	3: 20,008,886	W838R	probably damaging	Het
Ide	A	T	19: 37,295,944	W527R		Het
Ighe	A	T	12: 113,272,355	I117N		Het
Ighv1-50	T	C	12: 115,119,776	E108G	probably benign	Het
Ivl	G	A	3: 92,572,231	P176S	probably damaging	Het
Lamb2	T	A	9: 108,484,084	L605Q	possibly damaging	Het
Lgi3	G	A	14: 70,533,392	R157H	probably damaging	Het
Lrp1b	G	T	2: 41,375,994	C1053*	probably null	Het
Mcpt9	A	T	14: 56,026,988	S217T	probably damaging	Het
Mgat4c	T	G	10: 102,388,496	N190K	probably damaging	Het
Mknk1	T	A	4: 115,864,592	V111D	probably damaging	Het
Mmp11	T	C	10: 75,928,446	T62A	probably benign	Het
Mmp1b	C	A	9: 7,385,014	V212F	probably damaging	Het
Mmp7	A	G	9: 7,697,586		probably null	Het
Muc5b	C	T	7: 141,863,967	T3550M	possibly damaging	Het
Nbeal1	G	C	1: 60,237,151	V684L	probably benign	Het
Nphp3	A	T	9: 104,004,837	K169*	probably null	Het
Npy6r	G	T	18: 44,275,721	V70F	probably benign	Het
Nsun2	T	A	13: 69,626,553		probably null	Het
Oplah	T	A	15: 76,302,660	I652F	probably benign	Het
Pcdh18	T	C	3: 49,755,822	N348S	probably damaging	Het
Pcdhb5	T	A	18: 37,321,356	V263D	probably damaging	Het
Pdk4	A	G	6: 5,491,068		probably null	Het
Pfkp	C	A	13: 6,602,781	V434F	probably benign	Het
Phospho1	G	A	11: 95,830,906	R134H	probably damaging	Het
Polg2	G	T	11: 106,772,746	Q374K	probably benign	Het
Ptpra	T	C	2: 130,537,651		probably null	Het
Rassf3	C	T	10: 121,416,147	E120K	probably benign	Het
Reln	A	T	5: 22,106,097	S273T	probably damaging	Het
Scarb1	C	T	5: 125,284,025	A133T	probably benign	Het
Scn3a	T	A	2: 65,483,142	K1142N	probably damaging	Het
Sema3c	G	A	5: 17,694,703	V398I	probably benign	Het
Serpine1	C	A	5: 137,071,064	Q80H	probably damaging	Het
Sh3gl1	G	A	17: 56,017,646	T334M	probably damaging	Het
Smg7	T	C	1: 152,861,825	N122D	probably benign	Het
Speer4b	T	C	5: 27,498,710	I144V	probably benign	Het
Spire2	T	A	8: 123,369,250	D671E	probably benign	Het
Sspo	A	T	6: 48,501,095	H5144L	probably benign	Het
Sstr2	A	T	11: 113,625,353	Q366L	probably damaging	Het
Ssu72	T	C	4: 155,731,393	F98S	probably damaging	Het
Syde2	C	T	3: 146,007,115	Q1003*	probably null	Het
Tapbp	G	A	17: 33,925,487	A186T	possibly damaging	Het
Tcf12	T	A	9: 71,883,103		probably null	Het
Tnfrsf22	A	T	7: 143,640,819	C124S	probably damaging	Het
Txlnb	A	T	10: 17,827,798	T235S	possibly damaging	Het
Uaca	T	C	9: 60,870,413	L694P	probably damaging	Het
Unc13a	T	A	8: 71,630,553	N1620Y	probably damaging	Het
Vmn2r10	C	T	5: 109,003,334	C138Y	probably damaging	Het
Vmn2r111	T	C	17: 22,559,051	N549S	possibly damaging	Het
Vmn2r28	T	A	7: 5,481,496	E568D	probably benign	Het
Vmn2r57	A	T	7: 41,448,471	H57Q	possibly damaging	Het
Vwa5b1	A	G	4: 138,581,612	S756P	probably benign	Het
Washc5	C	A	15: 59,352,501	E470*	probably null	Het
Xpot	A	T	10: 121,606,773	V508D	probably damaging	Het
Zfp616	A	T	11: 74,085,261	K785N	possibly damaging	Het
Zfp653	T	C	9: 22,065,899	N119D	probably damaging	Het
Zfp729b	A	G	13: 67,593,376	S257P	probably damaging	Het
Zfp82	T	A	7: 30,056,167	T497S	probably benign	Het
Znrf4	T	G	17: 56,512,305	M1L	probably benign	Het

Other mutations in Pcdhga1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R1074:Pcdhga1	UTSW	18	37825087	splice site	probably benign
R1869:Pcdhga1	UTSW	18	37840090	missense	probably damaging	0.98
R1871:Pcdhga1	UTSW	18	37840090	missense	probably damaging	0.98
R3723:Pcdhga1	UTSW	18	37662992	missense	possibly damaging	0.89
R3732:Pcdhga1	UTSW	18	37664123	missense	probably benign	0.00
R4243:Pcdhga1	UTSW	18	37663552	missense	probably damaging	1.00
R4245:Pcdhga1	UTSW	18	37663552	missense	probably damaging	1.00
R4424:Pcdhga1	UTSW	18	37662579	missense	probably damaging	0.97
R4898:Pcdhga1	UTSW	18	37662354	missense	possibly damaging	0.63
R4941:Pcdhga1	UTSW	18	37662606	missense	probably benign	0.10
R5021:Pcdhga1	UTSW	18	37663823	missense	probably damaging	1.00
R5765:Pcdhga1	UTSW	18	37663661	missense	probably benign	0.31
R6176:Pcdhga1	UTSW	18	37664229	missense	probably benign	0.22
R6380:Pcdhga1	UTSW	18	37662969	missense	probably damaging	1.00
R7062:Pcdhga1	UTSW	18	37825077	missense	probably damaging	1.00
R7266:Pcdhga1	UTSW	18	37839975	missense	possibly damaging	0.94
R7525:Pcdhga1	UTSW	18	37662228	missense	probably damaging	1.00
R7581:Pcdhga1	UTSW	18	37662177	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGCAGAGAAGCAATACCCTTG -3'
(R):5'- AGGGAGAAGCTTCATTTCATCCTC -3'

Sequencing Primer
(F):5'- GCAATACCCTTGATACCAGATTGAG -3'
(R):5'- CTCCATAAGGATGTTAAAGCTGACG -3'

Posted On

2019-05-15