Mutagenetix > Incidental Mutation

Incidental Mutation 'R4941:Pcdhga1'

383149

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga1

Ensembl Gene

ENSMUSG00000103144

Gene Name

protocadherin gamma subfamily A, 1

Synonyms

MMRRC Submission

042539-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R4941 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

37794846-37974926 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 37795659 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Isoleucine to Lysine at position 221 (I221K)

Ref Sequence

ENSEMBL: ENSMUSP00000141367 (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 benign
Transcript: ENSMUST00000194190
AA Change: I221K

PolyPhen 2 Score 0.101 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144
AA Change: I221K

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

probably benign
Transcript: ENSMUST00000194888
AA Change: I221K

PolyPhen 2 Score 0.101 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000141367
Gene: ENSMUSG00000103144
AA Change: I221K

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: 98.9%
3x: 98.0%
10x: 95.4%
20x: 89.0%

Validation Efficiency

97% (112/116)

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: 98 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A4galt	T	A	15: 83,112,529 (GRCm39)	I85F	probably damaging	Het
Abcc6	T	A	7: 45,661,947 (GRCm39)	I435F	probably benign	Het
Adam3	T	C	8: 25,167,332 (GRCm39)		probably benign	Het
Adrb3	T	C	8: 27,717,450 (GRCm39)	Y333C	probably damaging	Het
Ago4	A	T	4: 126,419,847 (GRCm39)	D43E	probably benign	Het
Agt	T	A	8: 125,283,727 (GRCm39)	Q464L	probably benign	Het
Amdhd1	A	T	10: 93,367,463 (GRCm39)	D230E	probably damaging	Het
Aplf	A	G	6: 87,645,405 (GRCm39)	I33T	probably damaging	Het
Aplf	A	T	6: 87,623,331 (GRCm39)	N249K	probably benign	Het
Arap2	A	G	5: 62,906,821 (GRCm39)	M66T	probably benign	Het
Atf4	T	C	15: 80,140,434 (GRCm39)		probably benign	Het
Bahcc1	A	C	11: 120,177,491 (GRCm39)	H2068P	probably benign	Het
Bcor	C	T	X: 11,906,725 (GRCm39)	R1551Q	probably damaging	Het
Bltp1	A	C	3: 36,971,851 (GRCm39)	H528P	probably damaging	Het
Bltp1	G	A	3: 36,974,050 (GRCm39)	S600N	probably benign	Het
Catsper1	C	A	19: 5,391,466 (GRCm39)	A616D	possibly damaging	Het
Cdkn3	A	G	14: 47,007,320 (GRCm39)	D159G	possibly damaging	Het
Cep162	T	C	9: 87,108,022 (GRCm39)		probably benign	Het
Clca3a1	T	A	3: 144,721,414 (GRCm39)	I386L	probably damaging	Het
Cldn10	G	A	14: 119,025,725 (GRCm39)	G53S	possibly damaging	Het
Cmtm3	T	C	8: 105,070,460 (GRCm39)	L73P	probably damaging	Het
Cnksr3	A	C	10: 7,102,925 (GRCm39)	L149R	probably benign	Het
Cope	T	C	8: 70,755,584 (GRCm39)		probably null	Het
Cpa6	T	A	1: 10,479,562 (GRCm39)	M224L	probably benign	Het
Cyp2d41-ps	T	C	15: 82,666,154 (GRCm39)		noncoding transcript	Het
Ddx55	T	A	5: 124,706,779 (GRCm39)	L592*	probably null	Het
Deup1	T	C	9: 15,499,323 (GRCm39)	M333V	probably benign	Het
Eif4a1	T	C	11: 69,558,640 (GRCm39)		probably benign	Het
Eif4g3	A	C	4: 137,897,876 (GRCm39)	D1026A	probably damaging	Het
Eif5b	T	C	1: 38,090,280 (GRCm39)	V1153A	probably damaging	Het
Ercc8	G	T	13: 108,297,301 (GRCm39)		probably benign	Het
Fam227a	C	A	15: 79,524,204 (GRCm39)		probably null	Het
Fat1	A	G	8: 45,489,312 (GRCm39)	I3505V	probably benign	Het
Fat3	T	G	9: 16,286,448 (GRCm39)	E1025A	probably damaging	Het
Fat4	C	T	3: 39,011,601 (GRCm39)	R2234W	probably damaging	Het
Fer1l4	G	T	2: 155,887,009 (GRCm39)	F634L	probably damaging	Het
Fetub	G	A	16: 22,756,624 (GRCm39)	V162I	probably benign	Het
Fgd4	T	C	16: 16,302,402 (GRCm39)	Q51R	probably benign	Het
Fgfr2	T	C	7: 129,800,175 (GRCm39)	H140R	probably benign	Het
Flt3	T	A	5: 147,293,185 (GRCm39)		probably null	Het
Gabrb1	A	G	5: 72,294,121 (GRCm39)	N465S	probably damaging	Het
Gapdhs	T	C	7: 30,432,691 (GRCm39)	I206V	probably benign	Het
Gkn3	C	T	6: 87,360,507 (GRCm39)	A163T	probably damaging	Het
Glp2r	T	C	11: 67,637,529 (GRCm39)		probably null	Het
Gm4956	T	A	1: 21,368,306 (GRCm39)		noncoding transcript	Het
Gtf2a1l	A	T	17: 89,022,350 (GRCm39)	D447V	probably damaging	Het
Hsd3b5	A	G	3: 98,526,379 (GRCm39)	W356R	probably damaging	Het
Idh2	A	T	7: 79,745,847 (GRCm39)	V335D	probably damaging	Het
Isyna1	T	C	8: 71,048,146 (GRCm39)	I184T	probably damaging	Het
Kcnh2	A	G	5: 24,536,085 (GRCm39)	S320P	probably damaging	Het
Klk14	G	A	7: 43,341,501 (GRCm39)	C51Y	probably damaging	Het
Kpna6	A	G	4: 129,541,825 (GRCm39)	F524S	probably damaging	Het
Lap3	A	T	5: 45,663,539 (GRCm39)	M338L	probably benign	Het
Lins1	T	C	7: 66,359,198 (GRCm39)		probably benign	Het
Llgl1	C	T	11: 60,600,394 (GRCm39)	P581L	probably benign	Het
Lrrc43	A	G	5: 123,639,126 (GRCm39)	D385G	probably benign	Het
Maf	T	C	8: 116,433,532 (GRCm39)	D24G	unknown	Het
Nell1	T	C	7: 49,712,386 (GRCm39)	S69P	probably benign	Het
Nkapd1	G	T	9: 50,518,809 (GRCm39)	Q268K	probably benign	Het
Or13p4	C	T	4: 118,547,089 (GRCm39)	V187I	possibly damaging	Het
Or2h1	C	T	17: 37,404,484 (GRCm39)	G94E	probably damaging	Het
Or2j6	T	A	7: 139,980,792 (GRCm39)	M56L	probably benign	Het
Or51af1	T	C	7: 103,141,458 (GRCm39)	D209G	probably damaging	Het
Or5an10	A	G	19: 12,276,260 (GRCm39)	S79P	possibly damaging	Het
Or8g54	T	C	9: 39,707,160 (GRCm39)	M163T	possibly damaging	Het
Oxld1	T	C	11: 120,347,862 (GRCm39)	T112A	probably benign	Het
Parp14	T	C	16: 35,666,403 (GRCm39)	N1210S	probably benign	Het
Pcdhb10	C	A	18: 37,545,887 (GRCm39)	T321K	probably benign	Het
Pcdhb8	C	T	18: 37,489,059 (GRCm39)	L246F	probably benign	Het
Pcdhga9	T	A	18: 37,871,185 (GRCm39)	V338E	probably damaging	Het
Pdcd11	T	C	19: 47,108,325 (GRCm39)	S1231P	probably damaging	Het
Pde6c	A	T	19: 38,140,013 (GRCm39)	L325F	probably damaging	Het
Pnpla7	T	A	2: 24,887,276 (GRCm39)		probably null	Het
Pparg	T	A	6: 115,467,071 (GRCm39)	V478E	probably damaging	Het
Ppib	T	C	9: 65,967,672 (GRCm39)	V42A	probably benign	Het
Ppox	T	C	1: 171,105,166 (GRCm39)	M341V	probably damaging	Het
Proc	T	C	18: 32,258,166 (GRCm39)	K260E	possibly damaging	Het
Ptpro	C	T	6: 137,369,763 (GRCm39)	P525L	probably damaging	Het
Rnf14	C	A	18: 38,441,435 (GRCm39)	A275E	probably damaging	Het
Scnn1b	C	T	7: 121,511,231 (GRCm39)	P306L	probably damaging	Het
Sec14l5	A	G	16: 4,994,364 (GRCm39)	E386G	probably damaging	Het
Sftpa1	T	A	14: 40,854,509 (GRCm39)	I32N	probably damaging	Het
Slc26a5	A	G	5: 22,025,384 (GRCm39)	I408T	probably damaging	Het
Slc7a13	A	G	4: 19,841,467 (GRCm39)	Y438C	probably damaging	Het
Spire1	T	C	18: 67,652,384 (GRCm39)	E231G	possibly damaging	Het
Stab1	T	A	14: 30,873,528 (GRCm39)	I1014F	probably benign	Het
Steap2	T	C	5: 5,727,651 (GRCm39)	Y228C	probably damaging	Het
Tmem131l	T	C	3: 83,806,546 (GRCm39)	T1487A	probably benign	Het
Tmem171	A	G	13: 98,828,803 (GRCm39)	F116L	possibly damaging	Het
Tmem215	T	C	4: 40,474,520 (GRCm39)	V199A	probably damaging	Het
Tmem45a	T	C	16: 56,642,652 (GRCm39)	N173S	possibly damaging	Het
Uqcrc2	C	T	7: 120,242,301 (GRCm39)	R148C	probably benign	Het
Vmn2r116	A	G	17: 23,620,116 (GRCm39)	K617E	probably damaging	Het
Xrcc6	T	C	15: 81,924,013 (GRCm39)	L229P	probably damaging	Het
Yju2	A	G	17: 56,271,149 (GRCm39)	D97G	possibly damaging	Het
Zfp184	A	G	13: 22,133,891 (GRCm39)	D46G	probably damaging	Het
Zfp790	T	A	7: 29,528,916 (GRCm39)	C534S	possibly damaging	Het
Zfp990	A	T	4: 145,263,407 (GRCm39)	N135I	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
R4424:Pcdhga1	UTSW	18	37,795,632 (GRCm39)	missense	probably damaging	0.97
R4898:Pcdhga1	UTSW	18	37,795,407 (GRCm39)	missense	possibly damaging	0.63
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'- GTGGGGATAAACTCACTTCAGAG -3'
(R):5'- TCCAACTGAAATTTCCGGACC -3'

Sequencing Primer
(F):5'- GGGGATAAACTCACTTCAGAGCTACC -3'
(R):5'- CACACTGTGGTCTACCTTGTGAAAG -3'

Posted On

2016-04-27