Mutagenetix > Incidental Mutation

Incidental Mutation 'R8400:Pcdhac1'

647837

Institutional Source

Beutler Lab

Gene Symbol

Pcdhac1

Ensembl Gene

ENSMUSG00000103255

Gene Name

protocadherin alpha subfamily C, 1

Synonyms

CNRc1

MMRRC Submission

067763-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R8400 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37223189-37320710 bp(+) (GRCm39)

Type of Mutation

nonsense

DNA Base Change (assembly)

T to A at 37225453 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Stop codon at position 755 (Y755*)

Ref Sequence

ENSEMBL: ENSMUSP00000007584 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000007584] [ENSMUST00000047614] [ENSMUST00000070797] [ENSMUST00000115657] [ENSMUST00000115658] [ENSMUST00000115659] [ENSMUST00000115661] [ENSMUST00000115662] [ENSMUST00000192168] [ENSMUST00000192295] [ENSMUST00000192447] [ENSMUST00000192503] [ENSMUST00000192512] [ENSMUST00000192631] [ENSMUST00000193389] [ENSMUST00000193777] [ENSMUST00000193839] [ENSMUST00000194038] [ENSMUST00000194544] [ENSMUST00000194751] [ENSMUST00000195590]

AlphaFold

Q91Y10

Predicted Effect

probably null
Transcript: ENSMUST00000007584
AA Change: Y755*

SMART Domains

Protein: ENSMUSP00000007584
Gene: ENSMUSG00000103255
AA Change: Y755*

Domain	Start	End	E-Value	Type
signal peptide	1	18	N/A	INTRINSIC
CA	45	122	3.59e-1	SMART
CA	146	231	6.32e-22	SMART
CA	255	338	5.18e-18	SMART
CA	362	443	9.73e-23	SMART
CA	467	554	4.24e-23	SMART
CA	584	662	1.11e-8	SMART
Pfam:Cadherin_C_2	682	773	1.1e-12	PFAM
Pfam:Cadherin_tail	813	947	5.4e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000047614

SMART Domains

Protein: ENSMUSP00000047609
Gene: ENSMUSG00000103310

Domain	Start	End	E-Value	Type
CA	19	131	3.78e-2	SMART
CA	155	240	3.26e-24	SMART
CA	264	348	6.37e-27	SMART
CA	372	453	3.31e-25	SMART
CA	477	563	6.18e-25	SMART
CA	594	676	5.6e-14	SMART
low complexity region	679	696	N/A	INTRINSIC
transmembrane domain	699	721	N/A	INTRINSIC
Pfam:Cadherin_tail	799	933	5.3e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000070797

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442

Domain	Start	End	E-Value	Type
CA	22	132	3.09e-2	SMART
CA	156	241	6.14e-20	SMART
CA	265	349	3.92e-27	SMART
CA	373	454	4.94e-24	SMART
CA	478	564	1e-24	SMART
CA	592	672	4.55e-14	SMART
transmembrane domain	694	716	N/A	INTRINSIC
Pfam:Cadherin_tail	797	931	5.3e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115657

SMART Domains

Protein: ENSMUSP00000111321
Gene: ENSMUSG00000102206

Domain	Start	End	E-Value	Type
CA	21	131	2.95e-2	SMART
CA	155	240	7.44e-19	SMART
CA	264	347	5.63e-28	SMART
CA	371	452	3.14e-26	SMART
CA	476	562	1.42e-24	SMART
CA	593	675	1.03e-12	SMART
transmembrane domain	697	719	N/A	INTRINSIC
low complexity region	783	794	N/A	INTRINSIC
low complexity region	918	942	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000115658

SMART Domains

Protein: ENSMUSP00000111322
Gene: ENSMUSG00000007440

Domain	Start	End	E-Value	Type
low complexity region	15	21	N/A	INTRINSIC
CA	46	132	6.34e-2	SMART
CA	156	241	4.65e-20	SMART
CA	265	349	1.25e-25	SMART
CA	373	454	9.22e-24	SMART
CA	478	564	4.3e-24	SMART
CA	595	678	5.07e-12	SMART
low complexity region	706	721	N/A	INTRINSIC
Pfam:Cadherin_tail	795	929	5.3e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115659

SMART Domains

Protein: ENSMUSP00000111323
Gene: ENSMUSG00000103770

Domain	Start	End	E-Value	Type
low complexity region	44	51	N/A	INTRINSIC
CA	75	161	2.46e-2	SMART
CA	185	270	8.1e-20	SMART
CA	294	378	1.69e-22	SMART
CA	402	483	1.52e-24	SMART
CA	507	593	5.68e-24	SMART
CA	624	705	6.69e-12	SMART
transmembrane domain	727	749	N/A	INTRINSIC
Pfam:Cadherin_tail	828	962	5.6e-58	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: ENSMUST00000115662

SMART Domains

Protein: ENSMUSP00000111326
Gene: ENSMUSG00000104148

Domain	Start	End	E-Value	Type
CA	45	131	6.34e-2	SMART
CA	155	240	2.98e-18	SMART
CA	264	348	2.17e-29	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	5.02e-25	SMART
CA	594	675	8.16e-16	SMART
transmembrane domain	695	717	N/A	INTRINSIC
low complexity region	916	940	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192168

SMART Domains

Protein: ENSMUSP00000142293
Gene: ENSMUSG00000103092

Domain	Start	End	E-Value	Type
CA	21	131	2.2e-2	SMART
CA	155	240	2.05e-21	SMART
CA	264	348	8.81e-21	SMART
CA	372	453	2.01e-24	SMART
CA	477	563	1.42e-24	SMART
CA	591	673	1.63e-15	SMART
transmembrane domain	693	715	N/A	INTRINSIC
low complexity region	902	926	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192295

SMART Domains

Protein: ENSMUSP00000142103
Gene: ENSMUSG00000104252

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	568	5.38e-1	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000192447

SMART Domains

Protein: ENSMUSP00000142270
Gene: ENSMUSG00000102206

Domain	Start	End	E-Value	Type
CA	21	131	1.5e-4	SMART
CA	155	240	3.6e-21	SMART
CA	264	347	2.8e-30	SMART
CA	371	452	1.5e-28	SMART
CA	476	562	6.8e-27	SMART
CA	593	675	4.9e-15	SMART
transmembrane domain	697	719	N/A	INTRINSIC
low complexity region	783	794	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192503

SMART Domains

Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312

Domain	Start	End	E-Value	Type
low complexity region	11	17	N/A	INTRINSIC
CA	42	128	3.78e-2	SMART
CA	152	237	8.94e-22	SMART
CA	261	345	3.74e-24	SMART
CA	369	450	1.09e-25	SMART
CA	474	560	1.42e-24	SMART
CA	588	670	2.96e-13	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	910	934	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192512

SMART Domains

Protein: ENSMUSP00000141408
Gene: ENSMUSG00000104252

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
low complexity region	915	939	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000192631

SMART Domains

Protein: ENSMUSP00000142156
Gene: ENSMUSG00000104318

Domain	Start	End	E-Value	Type
CA	21	131	2.58e-2	SMART
CA	155	240	4.27e-19	SMART
CA	264	348	1.42e-24	SMART
CA	372	453	9.36e-25	SMART
CA	477	563	1.42e-24	SMART
CA	594	671	4.03e-6	SMART
transmembrane domain	696	718	N/A	INTRINSIC
low complexity region	905	929	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193389

SMART Domains

Protein: ENSMUSP00000141459
Gene: ENSMUSG00000103707

Domain	Start	End	E-Value	Type
CA	21	131	5.67e-2	SMART
CA	155	240	4.72e-21	SMART
CA	264	348	1.9e-25	SMART
CA	372	453	3.31e-25	SMART
CA	477	563	1.42e-24	SMART
CA	594	676	5.91e-13	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000193777

SMART Domains

Protein: ENSMUSP00000141587
Gene: ENSMUSG00000103707

Domain	Start	End	E-Value	Type
CA	21	131	5.67e-2	SMART
CA	155	240	4.72e-21	SMART
CA	264	348	1.9e-25	SMART
CA	372	453	3.31e-25	SMART
CA	477	563	1.42e-24	SMART
CA	594	676	5.91e-13	SMART
low complexity region	914	938	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193839

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442

Domain	Start	End	E-Value	Type
CA	22	132	3.09e-2	SMART
CA	156	241	6.14e-20	SMART
CA	265	349	3.92e-27	SMART
CA	373	454	4.94e-24	SMART
CA	478	564	1e-24	SMART
CA	592	672	4.55e-14	SMART
transmembrane domain	694	716	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193856

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000194038

SMART Domains

Protein: ENSMUSP00000142159
Gene: ENSMUSG00000103800

Domain	Start	End	E-Value	Type
CA	20	131	6.34e-2	SMART
CA	155	240	4.27e-19	SMART
CA	264	348	2.04e-25	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	9.88e-24	SMART
CA	594	676	8.62e-15	SMART
transmembrane domain	699	721	N/A	INTRINSIC
low complexity region	914	938	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: ENSMUST00000194751

SMART Domains

Protein: ENSMUSP00000142285
Gene: ENSMUSG00000103707

Domain	Start	End	E-Value	Type
low complexity region	15	21	N/A	INTRINSIC
Pfam:Cadherin_2	29	112	4.5e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000195590

SMART Domains

Protein: ENSMUSP00000141355
Gene: ENSMUSG00000104148

Domain	Start	End	E-Value	Type
CA	45	131	6.34e-2	SMART
CA	155	240	2.98e-18	SMART
CA	264	348	2.17e-29	SMART
CA	372	453	2.84e-24	SMART
CA	477	563	5.02e-25	SMART
CA	594	675	8.16e-16	SMART
transmembrane domain	695	717	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.7%
20x: 99.0%

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 alpha gene cluster, one of three related gene clusters tandemly linked on chromosome five that demonstrate an unusual genomic organization similar to that of B-cell and T-cell receptor gene clusters. The alpha gene cluster is composed of 15 cadherin superfamily genes related to the mouse CNR genes and consists of 13 highly similar and 2 more distantly related coding sequences. The tandem array of 15 N-terminal exons, or variable exons, are followed by downstream C-terminal exons, or constant exons, which are shared by all genes in the cluster. The large, uninterrupted N-terminal exons each encode six cadherin ectodomains while the C-terminal exons encode the cytoplasmic domain. These neural cadherin-like cell adhesion proteins are integral plasma membrane proteins that most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been observed and additional variants have been suggested but their full-length nature has yet to be determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a reporter allele are viable and fertile with no apparent gross phenotype. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 47 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca13	G	A	11: 9,243,925 (GRCm39)	M1929I	probably benign	Het
Abca13	T	C	11: 9,248,218 (GRCm39)	I2655T	probably damaging	Het
Acad10	A	G	5: 121,764,268 (GRCm39)	V887A	possibly damaging	Het
Acot10	T	C	15: 20,666,258 (GRCm39)	E161G	possibly damaging	Het
Astn1	C	T	1: 158,484,670 (GRCm39)	P919L	probably benign	Het
Atp1a4	T	A	1: 172,062,061 (GRCm39)	D688V	probably damaging	Het
C4bp	C	A	1: 130,564,484 (GRCm39)	C400F	probably damaging	Het
Col6a6	A	C	9: 105,651,995 (GRCm39)	D1005E	probably damaging	Het
Csnk1g3	C	T	18: 54,086,360 (GRCm39)	R422C	probably benign	Het
Cutc	T	C	19: 43,741,644 (GRCm39)	S15P	probably benign	Het
Dgkb	T	C	12: 38,652,837 (GRCm39)		probably null	Het
Disc1	T	C	8: 125,959,732 (GRCm39)	V748A	probably benign	Het
Dmbt1	C	G	7: 130,684,317 (GRCm39)	D778E	unknown	Het
Dmxl2	T	C	9: 54,291,037 (GRCm39)	Y2471C	probably benign	Het
Fam185a	T	A	5: 21,643,814 (GRCm39)	N243K	probably benign	Het
Fchsd2	A	T	7: 100,902,780 (GRCm39)	Q386L	possibly damaging	Het
Gm904	C	A	13: 50,797,453 (GRCm39)	P49Q	probably damaging	Het
H2-Q10	C	T	17: 35,781,374 (GRCm39)	R59C	probably damaging	Het
Ier5l	A	G	2: 30,363,105 (GRCm39)	Y307H	possibly damaging	Het
Kmt2e	C	A	5: 23,702,090 (GRCm39)	T906K	probably benign	Het
Kndc1	C	T	7: 139,493,434 (GRCm39)	R467W	probably damaging	Het
Muc5ac	C	A	7: 141,364,213 (GRCm39)	T2508K	probably damaging	Het
Nlrp9a	A	T	7: 26,264,431 (GRCm39)	M784L	probably benign	Het
Nlrp9b	T	A	7: 19,757,937 (GRCm39)	C391*	probably null	Het
Nubp2	A	C	17: 25,103,439 (GRCm39)	M146R	probably damaging	Het
Or10q3	T	A	19: 11,848,578 (GRCm39)	M1L	probably damaging	Het
Or1a1b	C	T	11: 74,097,221 (GRCm39)	V274M	possibly damaging	Het
Or2ag1b	T	A	7: 106,288,876 (GRCm39)	S21C	probably benign	Het
Or2b2	G	A	13: 21,888,085 (GRCm39)	V305M	probably benign	Het
Or4k45	A	T	2: 111,395,747 (GRCm39)	L14H	probably damaging	Het
Or7e166	A	T	9: 19,624,389 (GRCm39)	N89Y	probably benign	Het
Otud1	T	C	2: 19,663,189 (GRCm39)	V106A	possibly damaging	Het
Pkd1l3	C	T	8: 110,350,520 (GRCm39)	P455L	possibly damaging	Het
Ptprb	GAGACCCTCGGGAGCACTGCAGAGACCCTCAGGAACACTGCAAAGACCCTCGGGAGCACTGCAGAGACCCTCAGGAACACTGCAAAGACCCTCGGGAGCACTGCAGAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT	GAGACCCTCGGGAGCACTGCAGAGACCCTCAGGAACACTGCAAAGACCCTCGGGAGCACTGCAGAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACTGCAAAGACCCTCGGGAGCACT	10: 116,119,477 (GRCm39)		probably benign	Het
Samhd1	T	C	2: 156,941,353 (GRCm39)	E648G	probably benign	Het
Smarca5	T	C	8: 81,435,756 (GRCm39)	T794A	probably benign	Het
Spc24	A	T	9: 21,669,026 (GRCm39)	L87H	probably damaging	Het
Sppl2b	TGTCACAGGT	TGT	10: 80,701,903 (GRCm39)		probably null	Het
Stra6l	G	A	4: 45,864,905 (GRCm39)	R77Q	probably damaging	Het
Tdrd1	G	A	19: 56,837,081 (GRCm39)	V472M	probably benign	Het
Tsc2	A	T	17: 24,823,961 (GRCm39)	I948K	possibly damaging	Het
Ttc39d	T	C	17: 80,523,434 (GRCm39)	V31A	probably benign	Het
Vmn1r158	A	T	7: 22,489,305 (GRCm39)	C301*	probably null	Het
Vmn2r22	A	T	6: 123,614,486 (GRCm39)	L368*	probably null	Het
Vmn2r79	A	G	7: 86,651,308 (GRCm39)	T236A	probably benign	Het
Vwa1	T	C	4: 155,857,225 (GRCm39)	H191R	probably benign	Het
Zdbf2	T	A	1: 63,344,135 (GRCm39)	V838E	possibly damaging	Het

Other mutations in Pcdhac1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
G1patch:Pcdhac1	UTSW	18	37,223,381 (GRCm39)	missense	probably damaging	1.00
R2418:Pcdhac1	UTSW	18	37,224,381 (GRCm39)	missense	probably benign	0.12
R2419:Pcdhac1	UTSW	18	37,224,381 (GRCm39)	missense	probably benign	0.12
R3876:Pcdhac1	UTSW	18	37,224,945 (GRCm39)	missense	probably damaging	1.00
R4234:Pcdhac1	UTSW	18	37,224,011 (GRCm39)	missense	probably damaging	1.00
R4515:Pcdhac1	UTSW	18	37,224,432 (GRCm39)	missense	probably damaging	1.00
R4722:Pcdhac1	UTSW	18	37,224,933 (GRCm39)	missense	probably damaging	1.00
R4804:Pcdhac1	UTSW	18	37,224,231 (GRCm39)	missense	possibly damaging	0.67
R4996:Pcdhac1	UTSW	18	37,225,580 (GRCm39)	nonsense	probably null
R5093:Pcdhac1	UTSW	18	37,223,595 (GRCm39)	missense	probably damaging	1.00
R5111:Pcdhac1	UTSW	18	37,224,558 (GRCm39)	missense	probably damaging	1.00
R5116:Pcdhac1	UTSW	18	37,224,500 (GRCm39)	missense	probably damaging	1.00
R5203:Pcdhac1	UTSW	18	37,224,243 (GRCm39)	missense	probably damaging	1.00
R5659:Pcdhac1	UTSW	18	37,225,470 (GRCm39)	missense	probably damaging	1.00
R5679:Pcdhac1	UTSW	18	37,225,530 (GRCm39)	missense	probably damaging	1.00
R5765:Pcdhac1	UTSW	18	37,223,372 (GRCm39)	nonsense	probably null
R6536:Pcdhac1	UTSW	18	37,223,367 (GRCm39)	missense	probably benign	0.00
R6725:Pcdhac1	UTSW	18	37,223,381 (GRCm39)	missense	probably damaging	1.00
R6764:Pcdhac1	UTSW	18	37,223,732 (GRCm39)	missense	probably damaging	1.00
R6772:Pcdhac1	UTSW	18	37,223,289 (GRCm39)	missense	probably benign	0.05
R6870:Pcdhac1	UTSW	18	37,225,140 (GRCm39)	missense	probably damaging	1.00
R7426:Pcdhac1	UTSW	18	37,225,550 (GRCm39)	missense	probably benign
R7809:Pcdhac1	UTSW	18	37,224,009 (GRCm39)	missense	possibly damaging	0.55
R8088:Pcdhac1	UTSW	18	37,224,807 (GRCm39)	missense	possibly damaging	0.74
R8201:Pcdhac1	UTSW	18	37,223,892 (GRCm39)	missense	probably benign	0.16
R8787:Pcdhac1	UTSW	18	37,224,942 (GRCm39)	missense	probably damaging	1.00
R9349:Pcdhac1	UTSW	18	37,224,021 (GRCm39)	missense	possibly damaging	0.50
R9733:Pcdhac1	UTSW	18	37,225,506 (GRCm39)	missense	probably benign
Z1088:Pcdhac1	UTSW	18	37,225,619 (GRCm39)	missense	probably damaging	0.97
Z1088:Pcdhac1	UTSW	18	37,225,243 (GRCm39)	missense	probably damaging	1.00
Z1177:Pcdhac1	UTSW	18	37,225,476 (GRCm39)	missense	possibly damaging	0.90

Predicted Primers

PCR Primer
(F):5'- TTTCTGCCCGGAACTTGTAC -3'
(R):5'- GGCTTCCACATTTGAATGATCC -3'

Sequencing Primer
(F):5'- CCGGAACTTGTACTTGATAATAGCCC -3'
(R):5'- AATGATCCCCTTTCCTATTCCGAATC -3'

Posted On

2020-09-02