Mutagenetix > Incidental Mutation

Incidental Mutation 'R6329:Pcdha1'

509438

Institutional Source

Beutler Lab

Gene Symbol

Pcdha1

Ensembl Gene

ENSMUSG00000103442

Gene Name

protocadherin alpha 1

Synonyms

MMRRC Submission

044483-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6329 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37063338-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 37065301 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 655 (P655L)

Ref Sequence

ENSEMBL: ENSMUSP00000142308 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000193839]

AlphaFold

Q91Y21

Predicted Effect

probably damaging
Transcript: ENSMUST00000070797
AA Change: P655L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442
AA Change: P655L

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

noncoding transcript
Transcript: ENSMUST00000192440

Predicted Effect

probably damaging
Transcript: ENSMUST00000193839
AA Change: P655L

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442
AA Change: P655L

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

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.3%
20x: 97.6%

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 null allele are viable and fertile. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930579F01Rik	T	C	3: 137,879,457 (GRCm39)	H72R	probably damaging	Het
Abca13	A	T	11: 9,227,937 (GRCm39)	N660I	probably damaging	Het
Actr8	C	T	14: 29,715,041 (GRCm39)	R619*	probably null	Het
Adam18	C	A	8: 25,104,843 (GRCm39)	G657V	probably damaging	Het
Adcyap1	A	G	17: 93,510,227 (GRCm39)	E85G	probably benign	Het
Akr1c14	A	G	13: 4,137,302 (GRCm39)	Y305C	probably damaging	Het
Ankdd1b	T	A	13: 96,591,388 (GRCm39)	H37L	possibly damaging	Het
Ap4e1	T	C	2: 126,903,636 (GRCm39)	L846P	probably benign	Het
Aqp9	A	T	9: 71,039,966 (GRCm39)	Y105*	probably null	Het
Arid1b	C	T	17: 5,387,538 (GRCm39)	Q1664*	probably null	Het
Aup1	A	G	6: 83,031,588 (GRCm39)		probably benign	Het
Bnip1	C	A	17: 27,005,684 (GRCm39)	S64*	probably null	Het
Calcr	T	A	6: 3,687,621 (GRCm39)	Q422L	probably damaging	Het
Ccdc162	T	A	10: 41,539,147 (GRCm39)	D407V	possibly damaging	Het
Ccdc66	G	T	14: 27,208,441 (GRCm39)	S760R	probably benign	Het
Cd22	T	A	7: 30,577,193 (GRCm39)	E38V	probably damaging	Het
Cggbp1	T	C	16: 64,676,383 (GRCm39)	Y150H	probably damaging	Het
Chd3	T	C	11: 69,252,510 (GRCm39)	K263R	possibly damaging	Het
Col4a2	T	A	8: 11,496,238 (GRCm39)	F1620I	probably damaging	Het
Col6a2	T	C	10: 76,435,662 (GRCm39)	T858A	probably benign	Het
Dnah7a	T	A	1: 53,580,273 (GRCm39)	D1554V	probably damaging	Het
Dnajc25	A	T	4: 59,013,678 (GRCm39)	Q132L	probably benign	Het
Dnase1l1	C	T	X: 73,320,644 (GRCm39)		probably null	Homo
Ehbp1l1	A	C	19: 5,768,795 (GRCm39)	I836S	possibly damaging	Het
Elf1	A	G	14: 79,810,779 (GRCm39)	Q288R	possibly damaging	Het
Fbn1	C	A	2: 125,150,393 (GRCm39)	V2608L	possibly damaging	Het
Frmpd1	T	C	4: 45,268,551 (GRCm39)	I232T	possibly damaging	Het
Fuca1	T	A	4: 135,662,137 (GRCm39)	I355N	probably damaging	Het
Gcnt4	A	G	13: 97,083,781 (GRCm39)	D359G	probably damaging	Het
Gm5134	T	C	10: 75,790,494 (GRCm39)	M30T	possibly damaging	Het
Grk1	T	G	8: 13,455,704 (GRCm39)	L196R	probably damaging	Het
Igkv14-126	A	C	6: 67,873,548 (GRCm39)	D92A	probably damaging	Het
Kmt2c	A	G	5: 25,520,600 (GRCm39)	S1837P	probably benign	Het
Lhx4	T	A	1: 155,578,300 (GRCm39)	T281S	probably benign	Het
Lrrc55	G	T	2: 85,026,653 (GRCm39)	H124N	probably benign	Het
Marchf8	T	A	6: 116,383,277 (GRCm39)	I566N	possibly damaging	Het
Mycbp2	G	A	14: 103,393,288 (GRCm39)	A3091V	probably benign	Het
Nlrp4b	A	G	7: 10,458,847 (GRCm39)	N355S	probably benign	Het
Nmur2	A	G	11: 55,920,411 (GRCm39)	V278A	probably benign	Het
Nod1	T	C	6: 54,921,689 (GRCm39)	M210V	probably benign	Het
Nt5c1b	T	A	12: 10,422,138 (GRCm39)	C63*	probably null	Het
Or1e1f	A	G	11: 73,855,568 (GRCm39)	I45V	possibly damaging	Het
Or1j17	A	T	2: 36,578,694 (GRCm39)	K227*	probably null	Het
Or4g7	C	T	2: 111,309,573 (GRCm39)	A148V	possibly damaging	Het
Or5d37	G	A	2: 87,924,008 (GRCm39)	P91S	probably damaging	Het
Or7g21	A	C	9: 19,032,253 (GRCm39)	M1L	probably benign	Het
Or8b37	T	C	9: 37,959,121 (GRCm39)	V201A	probably benign	Het
Or8g24	C	T	9: 38,989,199 (GRCm39)	V281I	probably benign	Het
Osbp2	T	A	11: 3,665,153 (GRCm39)	S517C	probably damaging	Het
Pdcd6	A	G	13: 74,452,098 (GRCm39)	Y181H	probably damaging	Het
Perp	G	A	10: 18,731,502 (GRCm39)	G154S	probably damaging	Het
Perp	G	T	10: 18,731,503 (GRCm39)	G154V	probably damaging	Het
Pira13	T	C	7: 3,825,850 (GRCm39)	T340A	probably damaging	Het
Prokr1	T	G	6: 87,558,774 (GRCm39)	T204P	possibly damaging	Het
Prpf3	A	T	3: 95,739,890 (GRCm39)	C630S	probably damaging	Het
Pter	C	A	2: 12,985,359 (GRCm39)	H230N	probably damaging	Het
Ptprs	A	T	17: 56,724,427 (GRCm39)	Y1167*	probably null	Het
Rad54l2	T	C	9: 106,595,121 (GRCm39)	I279V	possibly damaging	Het
Rora	T	A	9: 69,280,468 (GRCm39)	L347Q	probably damaging	Het
Runx1t1	T	G	4: 13,785,136 (GRCm39)	M1R	probably null	Het
Sdcbp	A	G	4: 6,381,064 (GRCm39)	S70G	probably benign	Het
Serpinb12	A	G	1: 106,881,493 (GRCm39)	Y210C	probably damaging	Het
Sipa1	T	C	19: 5,701,517 (GRCm39)	E1015G	probably damaging	Het
Slc15a2	A	C	16: 36,572,144 (GRCm39)	L740R	possibly damaging	Het
Specc1	A	G	11: 62,047,379 (GRCm39)	E916G	probably damaging	Het
Spta1	T	C	1: 174,041,743 (GRCm39)	I1371T	possibly damaging	Het
Tagln3	T	C	16: 45,533,365 (GRCm39)	M130V	probably benign	Het
Tchh	A	T	3: 93,353,752 (GRCm39)	E1064V	unknown	Het
Tdp1	A	T	12: 99,880,330 (GRCm39)	S464C	probably damaging	Het
Tdp1	G	C	12: 99,880,331 (GRCm39)	S464T	probably benign	Het
Tenm3	T	C	8: 48,729,884 (GRCm39)	Y1374C	probably damaging	Het
Tmprss3	A	T	17: 31,402,833 (GRCm39)	Y455*	probably null	Het
Ttc5	A	G	14: 51,003,385 (GRCm39)	V433A	possibly damaging	Het
Wnt5a	A	T	14: 28,240,449 (GRCm39)	R180*	probably null	Het
Zfp53	A	G	17: 21,728,372 (GRCm39)	D135G	probably benign	Het
Zfp619	T	A	7: 39,186,969 (GRCm39)	C1000S	probably damaging	Het
Zfp647	G	A	15: 76,796,285 (GRCm39)	P125L	probably damaging	Het

Other mutations in Pcdha1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdha1	APN	18	37,065,228 (GRCm39)	missense	probably damaging	0.99
R0062:Pcdha1	UTSW	18	37,139,681 (GRCm39)	missense	probably benign	0.08
R0108:Pcdha1	UTSW	18	37,131,809 (GRCm39)	missense	probably benign
R0543:Pcdha1	UTSW	18	37,318,121 (GRCm39)	missense	probably damaging	1.00
R1599:Pcdha1	UTSW	18	37,318,290 (GRCm39)	missense	probably damaging	1.00
R1717:Pcdha1	UTSW	18	37,065,237 (GRCm39)	missense	probably benign	0.01
R2301:Pcdha1	UTSW	18	37,289,236 (GRCm39)	missense	probably damaging	1.00
R3038:Pcdha1	UTSW	18	37,064,064 (GRCm39)	missense	probably damaging	1.00
R3086:Pcdha1	UTSW	18	37,064,001 (GRCm39)	missense	possibly damaging	0.95
R3693:Pcdha1	UTSW	18	37,065,361 (GRCm39)	missense	possibly damaging	0.95
R3783:Pcdha1	UTSW	18	37,063,855 (GRCm39)	missense	probably damaging	1.00
R3881:Pcdha1	UTSW	18	37,064,454 (GRCm39)	missense	possibly damaging	0.91
R4012:Pcdha1	UTSW	18	37,064,189 (GRCm39)	missense	probably benign	0.02
R4540:Pcdha1	UTSW	18	37,064,680 (GRCm39)	missense	probably damaging	1.00
R4597:Pcdha1	UTSW	18	37,064,959 (GRCm39)	missense	possibly damaging	0.64
R4678:Pcdha1	UTSW	18	37,063,965 (GRCm39)	missense	probably benign	0.00
R4998:Pcdha1	UTSW	18	37,065,469 (GRCm39)	missense	probably damaging	1.00
R5466:Pcdha1	UTSW	18	37,065,312 (GRCm39)	missense	possibly damaging	0.73
R5518:Pcdha1	UTSW	18	37,065,415 (GRCm39)	missense	probably benign	0.23
R5673:Pcdha1	UTSW	18	37,063,726 (GRCm39)	missense	probably damaging	1.00
R5925:Pcdha1	UTSW	18	37,063,724 (GRCm39)	missense	probably damaging	1.00
R5942:Pcdha1	UTSW	18	37,063,444 (GRCm39)	missense	probably damaging	1.00
R5963:Pcdha1	UTSW	18	37,064,224 (GRCm39)	missense	probably damaging	0.99
R6034:Pcdha1	UTSW	18	37,063,651 (GRCm39)	missense	probably damaging	1.00
R6034:Pcdha1	UTSW	18	37,063,651 (GRCm39)	missense	probably damaging	1.00
R6107:Pcdha1	UTSW	18	37,065,354 (GRCm39)	missense	probably benign	0.00
R6479:Pcdha1	UTSW	18	37,064,509 (GRCm39)	missense	probably benign	0.28
R6503:Pcdha1	UTSW	18	37,064,724 (GRCm39)	missense	probably damaging	1.00
R6907:Pcdha1	UTSW	18	37,064,124 (GRCm39)	missense	probably benign	0.01
R7011:Pcdha1	UTSW	18	37,063,588 (GRCm39)	missense	probably damaging	1.00
R7030:Pcdha1	UTSW	18	37,292,326 (GRCm39)	missense	probably damaging	0.97
R7314:Pcdha1	UTSW	18	37,064,553 (GRCm39)	missense	probably damaging	0.99
R7343:Pcdha1	UTSW	18	37,063,702 (GRCm39)	missense	probably damaging	1.00
R7699:Pcdha1	UTSW	18	37,064,115 (GRCm39)	missense	probably damaging	0.98
R7700:Pcdha1	UTSW	18	37,064,115 (GRCm39)	missense	probably damaging	0.98
R7768:Pcdha1	UTSW	18	37,065,220 (GRCm39)	missense	probably damaging	1.00
R7780:Pcdha1	UTSW	18	37,065,511 (GRCm39)	missense	probably benign	0.28
R7800:Pcdha1	UTSW	18	37,064,426 (GRCm39)	missense	probably damaging	1.00
R7917:Pcdha1	UTSW	18	37,065,254 (GRCm39)	missense	possibly damaging	0.64
R8325:Pcdha1	UTSW	18	37,063,867 (GRCm39)	missense	possibly damaging	0.47
R8699:Pcdha1	UTSW	18	37,064,076 (GRCm39)	missense	probably benign	0.00
R9400:Pcdha1	UTSW	18	37,064,760 (GRCm39)	missense	probably benign	0.43
R9513:Pcdha1	UTSW	18	37,065,286 (GRCm39)	missense	probably benign	0.26
R9746:Pcdha1	UTSW	18	37,065,713 (GRCm39)	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- ACTGGTGTCACGGACAATGG -3'
(R):5'- AGCACTAACAGGCTGGACAC -3'

Sequencing Primer
(F):5'- CATGTGGTGACAAAGGTGCGC -3'
(R):5'- CTGGACACGGCACAGATG -3'

Posted On

2018-04-02