Mutagenetix > Incidental Mutations

Incidental Mutation 'R5615:Pcdhga12'

438220

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga12

Ensembl Gene

ENSMUSG00000102428

Gene Name

protocadherin gamma subfamily A, 12

Synonyms

pc2c, Pcdh13

Accession Numbers

Is this an essential gene?

Probably non essential (E-score: 0.235) question?

Stock #

R5615 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

37765580-37841873 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to G at 37768079 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Serine to Alanine at position 655 (S655A)

Ref Sequence

ENSEMBL: ENSMUSP00000036359 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000003599] [ENSMUST00000044851] [ENSMUST00000061279] [ENSMUST00000066149] [ENSMUST00000073447] [ENSMUST00000091935] [ENSMUST00000115661] [ENSMUST00000192511] [ENSMUST00000192535] [ENSMUST00000192931] [ENSMUST00000193404] [ENSMUST00000193414] [ENSMUST00000193869] [ENSMUST00000208907] [ENSMUST00000194190] [ENSMUST00000194418] [ENSMUST00000194544] [ENSMUST00000195363] [ENSMUST00000195764] [ENSMUST00000195112] [ENSMUST00000195823] [ENSMUST00000194928]

AlphaFold

Q91XY7

Predicted Effect

probably benign
Transcript: ENSMUST00000003599

SMART Domains

Protein: ENSMUSP00000003599
Gene: ENSMUSG00000103088

Domain	Start	End	E-Value	Type
CA	47	131	8.06e-6	SMART
CA	155	240	2.29e-19	SMART
CA	264	345	3.36e-26	SMART
CA	369	450	4.94e-24	SMART
CA	474	560	7.6e-25	SMART
CA	591	672	9.18e-10	SMART
Pfam:Cadherin_C_2	687	768	3.5e-20	PFAM
Pfam:Cadherin_tail	807	930	8.1e-38	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000044851
AA Change: S655A

PolyPhen 2 Score 0.984 (Sensitivity: 0.74; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000036359
Gene: ENSMUSG00000102428
AA Change: S655A

Domain	Start	End	E-Value	Type
low complexity region	12	23	N/A	INTRINSIC
CA	45	131	3.28e-1	SMART
CA	155	240	1.8e-17	SMART
CA	264	345	9.22e-24	SMART
CA	369	450	1.28e-22	SMART
CA	474	560	1.09e-25	SMART
CA	591	669	9.24e-15	SMART
Pfam:Cadherin_C_2	688	772	3.6e-25	PFAM
Pfam:Cadherin_tail	809	932	8.1e-38	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000061279

SMART Domains

Protein: ENSMUSP00000058362
Gene: ENSMUSG00000102742

Domain	Start	End	E-Value	Type
CA	45	131	3.23e-2	SMART
CA	155	240	2.22e-17	SMART
CA	264	345	3.36e-26	SMART
CA	369	450	7.09e-25	SMART
CA	474	560	3.55e-25	SMART
CA	591	669	2.53e-12	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	914	933	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000066149

SMART Domains

Protein: ENSMUSP00000067728
Gene: ENSMUSG00000103897

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
CA	31	131	4.84e-2	SMART
CA	155	240	1.48e-22	SMART
CA	264	345	1.14e-23	SMART
CA	369	450	9.44e-21	SMART
CA	474	560	1.03e-26	SMART
CA	591	669	3.64e-13	SMART
Pfam:Cadherin_C_2	688	772	3e-25	PFAM
Pfam:Cadherin_tail	809	932	8.1e-38	PFAM

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: ENSMUST00000091935

SMART Domains

Protein: ENSMUSP00000089555
Gene: ENSMUSG00000102440

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
CA	32	132	8.37e-3	SMART
CA	156	241	5.51e-22	SMART
CA	265	346	8.27e-26	SMART
CA	370	451	1.4e-23	SMART
CA	475	561	2.97e-27	SMART
CA	592	670	1.18e-12	SMART
Pfam:Cadherin_C_2	688	772	3.9e-24	PFAM
Pfam:Cadherin_tail	809	932	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

noncoding transcript
Transcript: ENSMUST00000180922

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000192501

Predicted Effect

probably benign
Transcript: ENSMUST00000192511

SMART Domains

Protein: ENSMUSP00000141704
Gene: ENSMUSG00000103472

Domain	Start	End	E-Value	Type
CA	47	133	1.57e-2	SMART
CA	157	242	3.24e-19	SMART
CA	266	347	3.21e-23	SMART
CA	371	452	9.08e-23	SMART
CA	476	562	1.32e-24	SMART
CA	593	671	3.5e-15	SMART
transmembrane domain	694	716	N/A	INTRINSIC
low complexity region	916	935	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192535

SMART Domains

Protein: ENSMUSP00000142010
Gene: ENSMUSG00000103749

Domain	Start	End	E-Value	Type
low complexity region	17	25	N/A	INTRINSIC
CA	56	131	8e-3	SMART
CA	155	240	2.49e-20	SMART
CA	264	341	4.97e-29	SMART
CA	365	446	1.09e-25	SMART
CA	470	556	1.75e-24	SMART
CA	587	668	9.18e-10	SMART
transmembrane domain	687	709	N/A	INTRINSIC
low complexity region	907	926	N/A	INTRINSIC

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: ENSMUST00000193045

Predicted Effect

probably benign
Transcript: ENSMUST00000193404

SMART Domains

Protein: ENSMUSP00000141359
Gene: ENSMUSG00000102222

Domain	Start	End	E-Value	Type
CA	43	129	2.76e-2	SMART
CA	153	238	1.16e-20	SMART
CA	262	343	1.25e-25	SMART
CA	367	448	4.75e-26	SMART
CA	472	558	3.69e-23	SMART
CA	589	667	3.84e-12	SMART
transmembrane domain	690	712	N/A	INTRINSIC
low complexity region	911	930	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193414

SMART Domains

Protein: ENSMUSP00000141893
Gene: ENSMUSG00000103567

Domain	Start	End	E-Value	Type
CA	45	131	2.45e-1	SMART
CA	155	240	1.05e-18	SMART
CA	264	345	6.52e-24	SMART
CA	369	450	5.99e-23	SMART
CA	474	560	6.99e-24	SMART
CA	591	669	5.31e-15	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	913	932	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: ENSMUST00000208907

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

SMART Domains

Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677

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: ENSMUST00000195363

SMART Domains

Protein: ENSMUSP00000142227
Gene: ENSMUSG00000103585

Domain	Start	End	E-Value	Type
low complexity region	17	25	N/A	INTRINSIC
CA	56	131	1.47e-2	SMART
CA	155	240	1.23e-19	SMART
CA	264	343	5.54e-27	SMART
CA	367	448	5.09e-26	SMART
CA	472	558	1.98e-23	SMART
CA	589	670	1.3e-9	SMART
transmembrane domain	689	711	N/A	INTRINSIC
low complexity region	893	912	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000195764

SMART Domains

Protein: ENSMUSP00000142272
Gene: ENSMUSG00000103081

Domain	Start	End	E-Value	Type
signal peptide	1	29	N/A	INTRINSIC
CA	57	132	1.5e-4	SMART
CA	156	241	1.2e-20	SMART
CA	265	346	7.8e-29	SMART
CA	370	451	1.7e-26	SMART
CA	475	561	2.2e-26	SMART
CA	592	673	6.4e-12	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	911	930	N/A	INTRINSIC

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

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000195823

SMART Domains

Protein: ENSMUSP00000141803
Gene: ENSMUSG00000103793

Domain	Start	End	E-Value	Type
low complexity region	13	24	N/A	INTRINSIC
CA	45	131	2.41e-2	SMART
CA	155	240	5.77e-16	SMART
CA	264	345	1.1e-21	SMART
CA	369	450	2.75e-22	SMART
low complexity region	453	462	N/A	INTRINSIC
CA	474	560	9.22e-24	SMART
CA	591	669	2.4e-13	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	913	932	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194928

SMART Domains

Protein: ENSMUSP00000141997
Gene: ENSMUSG00000104063

Domain	Start	End	E-Value	Type
CA	47	131	2.48e-6	SMART
CA	155	240	1.57e-17	SMART
CA	264	343	1.29e-27	SMART
CA	367	448	9.14e-28	SMART
CA	472	558	1.24e-24	SMART
CA	589	670	3.73e-10	SMART
transmembrane domain	689	711	N/A	INTRINSIC
low complexity region	716	721	N/A	INTRINSIC
low complexity region	910	929	N/A	INTRINSIC

Coding Region Coverage

1x: 99.8%
3x: 99.5%
10x: 97.6%
20x: 92.4%

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: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610010F05Rik	A	T	11: 23,606,759	L407H	probably damaging	Het
Abca12	A	T	1: 71,307,059	L884H	probably damaging	Het
Ahr	A	G	12: 35,503,885	V745A	probably benign	Het
Ankrd17	A	T	5: 90,283,436	S830T	possibly damaging	Het
Aox1	A	G	1: 58,096,966	T1123A	probably benign	Het
Arhgef11	T	C	3: 87,722,485		probably null	Het
Bcas3	T	A	11: 85,470,761	C250S	probably damaging	Het
Bckdk	T	C	7: 127,907,317	I272T	probably damaging	Het
Cacna1e	T	C	1: 154,412,170	K1897E	probably damaging	Het
Cd180	A	T	13: 102,706,203	I586F	probably benign	Het
Cep290	A	G	10: 100,531,150	D1121G	probably damaging	Het
Clasrp	A	G	7: 19,586,447		probably benign	Het
Col27a1	G	T	4: 63,281,114	K912N	probably damaging	Het
Dock4	G	T	12: 40,649,480	R231L	probably benign	Het
Ell	G	A	8: 70,590,732	S505N	probably benign	Het
Ephb6	A	G	6: 41,619,291	T833A	probably benign	Het
Hemk1	T	A	9: 107,330,824		probably null	Het
Hjurp	GT	GTT	1: 88,266,524		probably null	Het
Hspa12a	T	C	19: 58,804,650	I368V	possibly damaging	Het
Igkv3-3	A	T	6: 70,687,230	T19S	probably benign	Het
Itpr1	G	A	6: 108,488,600	A2158T	possibly damaging	Het
Lancl2	T	C	6: 57,722,511	Y104H	probably damaging	Het
Leng8	G	T	7: 4,144,958	E634*	probably null	Het
Lrrk1	A	T	7: 66,287,615	C930S	probably damaging	Het
Lvrn	C	T	18: 46,850,328	S46L	possibly damaging	Het
Mcidas	G	A	13: 112,997,425	V148I	probably benign	Het
Mprip	A	T	11: 59,758,487	T1006S	probably benign	Het
Mrgprb3	T	A	7: 48,643,486	M106L	probably benign	Het
Mroh2a	GCCC	GC	1: 88,232,257		probably null	Het
Mtor	G	A	4: 148,538,276	V1938I	possibly damaging	Het
Muc2	A	G	7: 141,691,203	D46G	probably damaging	Het
Nfkb2	G	T	19: 46,307,567	E170D	probably benign	Het
Olfr1113	T	A	2: 87,213,739	F282L	probably benign	Het
Olfr811	A	T	10: 129,801,767	C253S	probably damaging	Het
Osbp2	C	T	11: 3,863,356	G171D	probably benign	Het
Otud6b	A	T	4: 14,818,187	M238K	possibly damaging	Het
Pcdhac2	G	A	18: 37,146,423	G819R	probably benign	Het
Pcdhac2	G	T	18: 37,146,424	G819V	probably benign	Het
Pkd1l3	A	G	8: 109,630,210	I756V	probably benign	Het
Plekhd1	T	A	12: 80,720,590	S251T	probably damaging	Het
Ppp2r1a	A	T	17: 20,958,987	T96S	probably benign	Het
Qser1	A	C	2: 104,789,694	S258A	possibly damaging	Het
Rsph4a	G	A	10: 33,909,328	A412T	probably benign	Het
Sass6	T	A	3: 116,607,486	C159S	probably benign	Het
Scaf4	T	C	16: 90,251,960	Q322R	unknown	Het
Sema6d	C	T	2: 124,656,901	H244Y	probably damaging	Het
Sigirr	T	G	7: 141,092,719	L163F	probably damaging	Het
Spata31d1c	C	A	13: 65,035,264	L207I	possibly damaging	Het
Tacstd2	A	G	6: 67,535,049	F220L	probably damaging	Het
Tdpoz4	A	T	3: 93,797,499	T368S	probably benign	Het
Tnxb	C	A	17: 34,683,418	Q1082K	probably damaging	Het
Trim41	GCCTAGGCGCCCA	G	11: 48,807,365		probably benign	Het
Trpm6	C	T	19: 18,829,933	R1014C	probably damaging	Het
Ugt1a10	TTCATCA	TTCA	1: 88,216,158		probably benign	Het
Vmn2r114	ATTT	ATT	17: 23,290,932		probably null	Het
Vmn2r61	A	G	7: 42,300,493	E779G	probably damaging	Het
Vmn2r61	T	A	7: 42,267,253	M430K	probably benign	Het
Zfp599	T	C	9: 22,253,869	D70G	probably benign	Het
Zmym1	A	T	4: 127,049,398	I301N	probably damaging	Het

Other mutations in Pcdhga12

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R3946:Pcdhga12	UTSW	18	37767629	missense	probably benign	0.00
R3964:Pcdhga12	UTSW	18	37767201	missense	probably benign
R4169:Pcdhga12	UTSW	18	37766414	missense	probably benign
R4363:Pcdhga12	UTSW	18	37766161	missense	probably benign
R4409:Pcdhga12	UTSW	18	37768085	missense	probably damaging	0.99
R4754:Pcdhga12	UTSW	18	37766551	missense	probably damaging	1.00
R4863:Pcdhga12	UTSW	18	37768281	missense	probably benign	0.36
R4890:Pcdhga12	UTSW	18	37768237	missense	possibly damaging	0.72
R5029:Pcdhga12	UTSW	18	37766811	missense	probably benign	0.11
R5114:Pcdhga12	UTSW	18	37768107	missense	probably benign	0.10
R5274:Pcdhga12	UTSW	18	37766422	nonsense	probably null
R5276:Pcdhga12	UTSW	18	37766675	missense	possibly damaging	0.92
R5389:Pcdhga12	UTSW	18	37766732	missense	probably damaging	1.00
R5454:Pcdhga12	UTSW	18	37766261	missense	possibly damaging	0.46
R5704:Pcdhga12	UTSW	18	37767369	missense	probably damaging	1.00
R5825:Pcdhga12	UTSW	18	37768503	missense	possibly damaging	0.84
R5982:Pcdhga12	UTSW	18	37768031	missense	probably damaging	1.00
R6810:Pcdhga12	UTSW	18	37767179	missense	probably benign	0.00
R7330:Pcdhga12	UTSW	18	37768386	missense	probably damaging	0.99
R7611:Pcdhga12	UTSW	18	37768425	missense	possibly damaging	0.94
R7976:Pcdhga12	UTSW	18	37768374	missense	probably damaging	1.00
R8354:Pcdhga12	UTSW	18	37768137	missense	possibly damaging	0.81
R8454:Pcdhga12	UTSW	18	37768137	missense	possibly damaging	0.81
R8487:Pcdhga12	UTSW	18	37767578	missense	probably damaging	0.99
R8911:Pcdhga12	UTSW	18	37767065	missense	possibly damaging	0.75
R8946:Pcdhga12	UTSW	18	37766658	missense	probably benign
R9093:Pcdhga12	UTSW	18	37766878	missense	possibly damaging	0.89
R9293:Pcdhga12	UTSW	18	37767887	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TGGCTATCTGGTGACAAAGG -3'
(R):5'- AAGTGAGAGGCTGCAACGTC -3'

Sequencing Primer
(F):5'- TGGCAGTGGACAGAGACTC -3'
(R):5'- GGCTGCAACGTCAGCCAATC -3'

Posted On

2016-10-26