Mutagenetix > Incidental Mutation

Incidental Mutation 'R7699:Pcdha1'

593895

Institutional Source

Beutler Lab

Gene Symbol

Pcdha1

Ensembl Gene

ENSMUSG00000103442

Gene Name

protocadherin alpha 1

Synonyms

MMRRC Submission

045760-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7699 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37063338-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 37064115 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 260 (T260A)

Ref Sequence

ENSEMBL: ENSMUSP00000068828 (fasta)

Gene Model

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

AlphaFold

Q91Y21

Predicted Effect

probably damaging
Transcript: ENSMUST00000070797
AA Change: T260A

PolyPhen 2 Score 0.981 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442
AA Change: T260A

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

possibly damaging
Transcript: ENSMUST00000193839
AA Change: T260A

PolyPhen 2 Score 0.956 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442
AA Change: T260A

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: 99.7%
20x: 99.1%

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: 80 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1810009A15Rik	T	C	19: 8,867,417 (GRCm39)	L72P	probably benign	Het
4930407I10Rik	C	A	15: 81,948,306 (GRCm39)	H734Q	probably benign	Het
Acadl	A	G	1: 66,877,522 (GRCm39)	V343A	possibly damaging	Het
Acot4	A	T	12: 84,090,011 (GRCm39)	D236V	probably damaging	Het
App	T	A	16: 84,837,197 (GRCm39)		probably null	Het
Arfgef1	G	A	1: 10,264,636 (GRCm39)	T470I	possibly damaging	Het
Arhgef5	T	C	6: 43,251,691 (GRCm39)	I814T	probably benign	Het
Atr	A	T	9: 95,757,743 (GRCm39)	R968*	probably null	Het
Bltp1	T	A	3: 37,028,321 (GRCm39)	N2329K	possibly damaging	Het
Bltp1	C	T	3: 37,080,303 (GRCm39)	S267L	probably benign	Het
Capn7	C	T	14: 31,074,401 (GRCm39)	T268I	probably benign	Het
Ccn1	C	T	3: 145,354,447 (GRCm39)	G155R	probably damaging	Het
Cubn	A	T	2: 13,352,989 (GRCm39)	F1916L	probably benign	Het
Cubn	A	G	2: 13,494,728 (GRCm39)	V107A	possibly damaging	Het
Cyp11b1	T	A	15: 74,707,691 (GRCm39)	T473S	probably damaging	Het
Dip2c	T	G	13: 9,709,347 (GRCm39)	S1396A	probably benign	Het
Dyrk1b	T	C	7: 27,883,737 (GRCm39)	Y198H	probably damaging	Het
Echdc2	G	T	4: 108,031,274 (GRCm39)	R206L	probably benign	Het
Ep400	C	T	5: 110,843,898 (GRCm39)	R1594Q	unknown	Het
Fmnl2	G	A	2: 52,926,520 (GRCm39)	R69Q		Het
Fry	T	A	5: 150,328,792 (GRCm39)	H1308Q	probably damaging	Het
Fyb2	T	A	4: 104,867,651 (GRCm39)	D667E	probably benign	Het
Gimap7	T	A	6: 48,700,791 (GRCm39)	Y126N	possibly damaging	Het
Gm1979	A	T	5: 26,205,178 (GRCm39)	W266R	probably damaging	Het
Gm28042	T	A	2: 119,870,197 (GRCm39)	M712K	possibly damaging	Het
Gm3238	A	G	10: 77,606,469 (GRCm39)	*231R	probably null	Het
Gm5592	C	A	7: 40,935,831 (GRCm39)	A111E	probably damaging	Het
Gm7694	A	G	1: 170,128,717 (GRCm39)	*271Q	probably null	Het
Ift81	T	C	5: 122,732,623 (GRCm39)	M304V	possibly damaging	Het
Igfals	T	C	17: 25,099,548 (GRCm39)	L213P	probably damaging	Het
Ints3	G	A	3: 90,329,111 (GRCm39)	P83S	probably benign	Het
Kcna10	T	G	3: 107,102,856 (GRCm39)	S496A	probably damaging	Het
Kmt2d	G	A	15: 98,741,600 (GRCm39)	A4520V	unknown	Het
Lemd3	A	T	10: 120,813,995 (GRCm39)	Y413N	probably damaging	Het
Lgr6	T	C	1: 134,923,770 (GRCm39)	N453S	probably damaging	Het
Lmtk3	A	C	7: 45,441,998 (GRCm39)	D352A	probably damaging	Het
Lrrc4c	T	C	2: 97,461,024 (GRCm39)	M550T	possibly damaging	Het
Maml2	A	T	9: 13,532,385 (GRCm39)	Q533L		Het
Mdn1	T	A	4: 32,741,344 (GRCm39)	D3815E	probably damaging	Het
Megf8	C	T	7: 25,029,353 (GRCm39)	A299V	possibly damaging	Het
Meis3	G	T	7: 15,911,481 (GRCm39)	E59D	probably benign	Het
Mppe1	A	G	18: 67,358,775 (GRCm39)	*398R	probably null	Het
Mtmr7	G	A	8: 41,059,927 (GRCm39)	A62V	possibly damaging	Het
Mtus1	T	A	8: 41,537,006 (GRCm39)	T237S	possibly damaging	Het
Ndfip2	T	A	14: 105,525,193 (GRCm39)	V158E	possibly damaging	Het
Nrbp2	T	G	15: 75,962,746 (GRCm39)	T53P	probably damaging	Het
Nrde2	G	A	12: 100,097,094 (GRCm39)	P902L	probably benign	Het
Or10ab5	T	A	7: 108,244,879 (GRCm39)	K301N	probably damaging	Het
Or11g24	T	A	14: 50,662,792 (GRCm39)	M272K	probably benign	Het
Or2y13	A	G	11: 49,415,381 (GRCm39)	Y277C	probably damaging	Het
Or51a10	T	A	7: 103,699,800 (GRCm39)		probably benign	Het
Or6c202	T	C	10: 128,995,924 (GRCm39)	M310V	probably benign	Het
Pdlim1	T	G	19: 40,238,102 (GRCm39)	K98N	probably damaging	Het
Phrf1	G	A	7: 140,834,842 (GRCm39)	G207R	unknown	Het
Pik3r6	A	G	11: 68,419,389 (GRCm39)	K124R	probably damaging	Het
Polr2b	T	A	5: 77,488,268 (GRCm39)	F823I	probably benign	Het
Prss58	T	C	6: 40,872,322 (GRCm39)	I234V	probably damaging	Het
Ptpn14	A	T	1: 189,597,608 (GRCm39)	N766I	probably benign	Het
Qrfprl	T	A	6: 65,429,940 (GRCm39)	I212N	probably benign	Het
Repin1	T	A	6: 48,574,756 (GRCm39)	S562T	probably damaging	Het
Rgr	C	T	14: 36,766,552 (GRCm39)	D165N	probably damaging	Het
Rho	T	C	6: 115,912,200 (GRCm39)	F221L	probably damaging	Het
Rictor	C	T	15: 6,801,635 (GRCm39)	S441L	probably benign	Het
Rnase2a	A	G	14: 51,493,248 (GRCm39)	I39T	probably damaging	Het
Rpl13a	T	G	7: 44,776,660 (GRCm39)	I43L	probably benign	Het
Rpp30	T	C	19: 36,066,558 (GRCm39)	V97A	probably benign	Het
Scube3	T	C	17: 28,386,023 (GRCm39)	Y755H	probably damaging	Het
Sec24a	A	T	11: 51,603,084 (GRCm39)	V788E	probably damaging	Het
Spns2	A	T	11: 72,380,443 (GRCm39)	L60*	probably null	Het
Strc	T	C	2: 121,202,229 (GRCm39)	N1213S	possibly damaging	Het
Tec	A	T	5: 72,943,367 (GRCm39)	I116N	possibly damaging	Het
Tll1	A	T	8: 64,546,988 (GRCm39)	D319E	probably benign	Het
Tmem121b	T	C	6: 120,470,388 (GRCm39)	T110A	unknown	Het
Tmem232	T	A	17: 65,572,213 (GRCm39)	I593F	probably damaging	Het
Tpp2	A	G	1: 44,009,626 (GRCm39)	I487V	probably benign	Het
Ubr4	C	A	4: 139,136,178 (GRCm39)	C934*	probably null	Het
Vmn1r68	A	G	7: 10,261,559 (GRCm39)	Y180H	probably benign	Het
Vmn2r25	T	C	6: 123,816,882 (GRCm39)	D233G	possibly damaging	Het
Wdr6	A	G	9: 108,453,560 (GRCm39)	W108R	possibly damaging	Het
Zng1	A	G	19: 24,920,045 (GRCm39)		probably null	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
R6329:Pcdha1	UTSW	18	37,065,301 (GRCm39)	missense	probably damaging	1.00
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
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'- ATCCCTTTCGCTTGAACTGAG -3'
(R):5'- GGGAGTCCCTTTATCAACTGC -3'

Sequencing Primer
(F):5'- CCCTTTCGCTTGAACTGAGAAAATC -3'
(R):5'- GTCCCTTTATCAACTGCCTTTATTTG -3'

Posted On

2019-11-12