Mutagenetix > Incidental Mutation

Incidental Mutation 'R4424:Pcdhga1'

327299

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga1

Ensembl Gene

ENSMUSG00000103144

Gene Name

protocadherin gamma subfamily A, 1

Synonyms

MMRRC Submission

041696-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4424 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37794846-37974926 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 37795632 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Leucine to Proline at position 212 (L212P)

Ref Sequence

ENSEMBL: ENSMUSP00000142062 (fasta)

Gene Model

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

AlphaFold

Q91XZ0

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000097608

SMART Domains

Protein: ENSMUSP00000095213
Gene: ENSMUSG00000073590

Domain	Start	End	E-Value	Type
transmembrane domain	15	37	N/A	INTRINSIC
transmembrane domain	57	79	N/A	INTRINSIC

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

noncoding transcript
Transcript: ENSMUST00000192137

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably damaging
Transcript: ENSMUST00000194190
AA Change: L212P

PolyPhen 2 Score 0.972 (Sensitivity: 0.77; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144
AA Change: L212P

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

noncoding transcript
Transcript: ENSMUST00000194328

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

possibly damaging
Transcript: ENSMUST00000194888
AA Change: L212P

PolyPhen 2 Score 0.824 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000141367
Gene: ENSMUSG00000103144
AA Change: L212P

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

0.9016

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.3%

Validation Efficiency

95% (69/73)

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: 66 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4933409G03Rik	A	T	2: 68,445,491 (GRCm39)		probably benign	Het
Aimp1	A	T	3: 132,373,253 (GRCm39)	L229Q	probably benign	Het
Ankrd16	T	A	2: 11,789,215 (GRCm39)	D267E	possibly damaging	Het
Apol11b	A	G	15: 77,522,133 (GRCm39)		probably null	Het
Arfgap1	C	A	2: 180,622,869 (GRCm39)	D327E	probably benign	Het
Arid3b	A	T	9: 57,741,151 (GRCm39)	D98E	probably benign	Het
Art2b	T	A	7: 101,229,129 (GRCm39)	I257F	probably benign	Het
Atp5f1a	T	A	18: 77,867,766 (GRCm39)		probably benign	Het
Carmil3	A	G	14: 55,738,928 (GRCm39)	T861A	probably benign	Het
Cep164	A	T	9: 45,691,002 (GRCm39)	F1259L	possibly damaging	Het
Cfap91	G	T	16: 38,140,727 (GRCm39)	P409T	probably damaging	Het
Chrnd	T	C	1: 87,123,512 (GRCm39)	V350A	probably benign	Het
Clcn7	T	C	17: 25,379,150 (GRCm39)	L744P	probably damaging	Het
Csl	T	A	10: 99,594,453 (GRCm39)	D204V	possibly damaging	Het
Cstdc3	A	G	16: 36,132,951 (GRCm39)	D76G	probably null	Het
Cyp2c29	G	T	19: 39,275,620 (GRCm39)	W20L	probably damaging	Het
Dhrs13	G	T	11: 77,927,951 (GRCm39)	G266*	probably null	Het
Dll3	T	C	7: 27,995,716 (GRCm39)	N362D	probably damaging	Het
Efcab3	T	G	11: 104,626,940 (GRCm39)		probably null	Het
Fanca	A	G	8: 124,015,532 (GRCm39)	V715A	probably benign	Het
Fhod1	T	C	8: 106,063,983 (GRCm39)		probably benign	Het
Fpr2	C	T	17: 18,113,394 (GRCm39)	P130L	probably damaging	Het
Glce	A	G	9: 61,967,535 (GRCm39)	Y539H	probably damaging	Het
Hfe	A	T	13: 23,890,866 (GRCm39)	V91E	probably benign	Het
Hoxd13	A	T	2: 74,500,301 (GRCm39)	K281*	probably null	Het
Ighv1-66	A	T	12: 115,557,157 (GRCm39)	W3R	probably damaging	Het
Impg2	G	A	16: 56,080,388 (GRCm39)	V622I	possibly damaging	Het
Jun	A	G	4: 94,939,084 (GRCm39)	M142T	probably benign	Het
Krt78	T	C	15: 101,856,375 (GRCm39)	T479A	probably benign	Het
Lama3	T	A	18: 12,652,929 (GRCm39)	C216*	probably null	Het
Lin54	G	T	5: 100,594,419 (GRCm39)	T582K	probably damaging	Het
Mapk11	A	G	15: 89,029,576 (GRCm39)		probably null	Het
Mindy3	A	G	2: 12,353,010 (GRCm39)	M397T	probably benign	Het
Mrpl41	T	C	2: 24,864,418 (GRCm39)	T85A	possibly damaging	Het
Msh6	T	A	17: 88,298,217 (GRCm39)	L1354*	probably null	Het
Mtmr12	T	C	15: 12,230,400 (GRCm39)	V41A	probably damaging	Het
Myh2	A	T	11: 67,083,551 (GRCm39)	Q1478L	probably benign	Het
Myo6	A	G	9: 80,195,320 (GRCm39)	K897E	probably benign	Het
Naprt	G	T	15: 75,764,605 (GRCm39)		probably null	Het
Nrl	G	A	14: 55,759,675 (GRCm39)	S84L	probably benign	Het
Nxf1	A	G	19: 8,744,128 (GRCm39)		probably benign	Het
Or8g2b	A	T	9: 39,751,652 (GRCm39)	R307S	possibly damaging	Het
Panx2	G	T	15: 88,952,423 (GRCm39)	V305F	probably benign	Het
Pik3ap1	G	A	19: 41,364,320 (GRCm39)	T133I	probably benign	Het
Ppat	A	G	5: 77,063,061 (GRCm39)	W517R	probably damaging	Het
Ppp1r16b	C	T	2: 158,599,174 (GRCm39)	T382I	probably benign	Het
Prkdc	G	A	16: 15,653,946 (GRCm39)	R3901H	probably damaging	Het
Prkdc	A	G	16: 15,591,603 (GRCm39)	K2694E	probably damaging	Het
Psma8	A	G	18: 14,854,247 (GRCm39)	I42M	probably damaging	Het
Ptprd	A	T	4: 76,021,200 (GRCm39)	M599K	probably benign	Het
Rnmt	A	G	18: 68,444,742 (GRCm39)	D237G	probably null	Het
Rpl31-ps17	C	T	12: 54,748,397 (GRCm39)		noncoding transcript	Het
Scaf11	G	A	15: 96,316,309 (GRCm39)	T1085I	possibly damaging	Het
Sec14l3	G	A	11: 4,016,210 (GRCm39)	R43Q	probably damaging	Het
Shc4	G	T	2: 125,494,442 (GRCm39)	T131K	probably benign	Het
Snx27	A	G	3: 94,469,330 (GRCm39)	F4L	probably benign	Het
Sorcs1	T	C	19: 50,367,379 (GRCm39)	T228A	probably damaging	Het
Spmap2l	T	C	5: 77,202,383 (GRCm39)	I268T	possibly damaging	Het
Sptan1	C	T	2: 29,919,721 (GRCm39)		probably benign	Het
Syvn1	C	T	19: 6,099,951 (GRCm39)		probably benign	Het
Tex47	G	T	5: 7,355,364 (GRCm39)	A182S	probably benign	Het
Tpcn1	T	C	5: 120,680,583 (GRCm39)	K549R	probably damaging	Het
Upf3a	C	A	8: 13,846,573 (GRCm39)	P318T	probably benign	Het
Zbtb40	A	T	4: 136,726,005 (GRCm39)	M518K	probably damaging	Het
Zcchc14	G	A	8: 122,378,680 (GRCm39)		probably benign	Het
Zfp687	G	A	3: 94,916,439 (GRCm39)	P861L	probably damaging	Het

Other mutations in Pcdhga1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
BB009:Pcdhga1	UTSW	18	37,796,513 (GRCm39)	missense	probably damaging	1.00
BB019:Pcdhga1	UTSW	18	37,796,513 (GRCm39)	missense	probably damaging	1.00
R1074:Pcdhga1	UTSW	18	37,958,140 (GRCm39)	splice site	probably benign
R1869:Pcdhga1	UTSW	18	37,973,143 (GRCm39)	missense	probably damaging	0.98
R1871:Pcdhga1	UTSW	18	37,973,143 (GRCm39)	missense	probably damaging	0.98
R3723:Pcdhga1	UTSW	18	37,796,045 (GRCm39)	missense	possibly damaging	0.89
R3732:Pcdhga1	UTSW	18	37,797,176 (GRCm39)	missense	probably benign	0.00
R4243:Pcdhga1	UTSW	18	37,796,605 (GRCm39)	missense	probably damaging	1.00
R4245:Pcdhga1	UTSW	18	37,796,605 (GRCm39)	missense	probably damaging	1.00
R4898:Pcdhga1	UTSW	18	37,795,407 (GRCm39)	missense	possibly damaging	0.63
R4941:Pcdhga1	UTSW	18	37,795,659 (GRCm39)	missense	probably benign	0.10
R5021:Pcdhga1	UTSW	18	37,796,876 (GRCm39)	missense	probably damaging	1.00
R5765:Pcdhga1	UTSW	18	37,796,714 (GRCm39)	missense	probably benign	0.31
R6176:Pcdhga1	UTSW	18	37,797,282 (GRCm39)	missense	probably benign	0.22
R6380:Pcdhga1	UTSW	18	37,796,022 (GRCm39)	missense	probably damaging	1.00
R7062:Pcdhga1	UTSW	18	37,958,130 (GRCm39)	missense	probably damaging	1.00
R7146:Pcdhga1	UTSW	18	37,795,164 (GRCm39)	missense	probably benign	0.04
R7266:Pcdhga1	UTSW	18	37,973,028 (GRCm39)	missense	possibly damaging	0.94
R7525:Pcdhga1	UTSW	18	37,795,281 (GRCm39)	missense	probably damaging	1.00
R7553:Pcdhga1	UTSW	18	37,882,735 (GRCm39)	splice site	probably null
R7581:Pcdhga1	UTSW	18	37,795,230 (GRCm39)	missense	probably damaging	1.00
R7932:Pcdhga1	UTSW	18	37,796,513 (GRCm39)	missense	probably damaging	1.00
R8330:Pcdhga1	UTSW	18	37,796,376 (GRCm39)	missense	probably benign	0.19
R8385:Pcdhga1	UTSW	18	37,795,149 (GRCm39)	missense	probably damaging	1.00
R8549:Pcdhga1	UTSW	18	37,966,386 (GRCm39)	makesense	probably null
R9147:Pcdhga1	UTSW	18	37,796,433 (GRCm39)	missense	possibly damaging	0.54
R9148:Pcdhga1	UTSW	18	37,796,433 (GRCm39)	missense	possibly damaging	0.54
R9192:Pcdhga1	UTSW	18	37,973,084 (GRCm39)	missense	probably damaging	1.00
R9336:Pcdhga1	UTSW	18	37,795,251 (GRCm39)	missense	probably damaging	0.97

Predicted Primers

PCR Primer
(F):5'- TCTCGGGCAAGACCTTGATG -3'
(R):5'- CACACTGTGGTCTACCTTGTGAAAG -3'

Sequencing Primer
(F):5'- CCTTGATGTGGGGATAAACTCAC -3'
(R):5'- AGTAGGTTACTCTGCCATTAGC -3'

Posted On

2015-07-07