Mutagenetix > Incidental Mutation

Incidental Mutation 'R7301:Pcdha3'

567019

Institutional Source

Beutler Lab

Gene Symbol

Pcdha3

Ensembl Gene

ENSMUSG00000102312

Gene Name

protocadherin alpha 3

Synonyms

MMRRC Submission

045405-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.116) question?

Stock #

R7301 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37079158-37320710 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 37079977 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Lysine at position 240 (E240K)

Ref Sequence

ENSEMBL: ENSMUSP00000141989 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000070797] [ENSMUST00000115662] [ENSMUST00000192503] [ENSMUST00000193839] [ENSMUST00000195590]

AlphaFold

Q91Y16

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: 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

possibly damaging
Transcript: ENSMUST00000192503
AA Change: E240K

PolyPhen 2 Score 0.564 (Sensitivity: 0.88; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000141989
Gene: ENSMUSG00000102312
AA Change: E240K

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: 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: 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: 100.0%
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]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsm3	G	A	7: 119,376,308 (GRCm39)	S345N	possibly damaging	Het
Agk	A	T	6: 40,306,451 (GRCm39)	T7S	possibly damaging	Het
Ankrd26	T	C	6: 118,488,624 (GRCm39)	E1345G	possibly damaging	Het
Atp1a3	T	A	7: 24,689,940 (GRCm39)	Y493F	probably benign	Het
Atxn2l	G	T	7: 126,093,383 (GRCm39)	Y791*	probably null	Het
Cacng8	C	A	7: 3,463,937 (GRCm39)	T363K	probably benign	Het
Camkmt	A	G	17: 85,738,921 (GRCm39)	T216A	probably benign	Het
Cd2ap	G	A	17: 43,140,904 (GRCm39)	R212*	probably null	Het
Cnppd1	A	G	1: 75,113,068 (GRCm39)	L400P	probably damaging	Het
Csmd2	C	A	4: 128,422,055 (GRCm39)	D2797E		Het
Ddx24	A	G	12: 103,385,709 (GRCm39)	M298T	possibly damaging	Het
Dpyd	T	C	3: 118,692,933 (GRCm39)	V359A	possibly damaging	Het
Dscam	T	C	16: 96,857,732 (GRCm39)	T93A	probably benign	Het
Eif2b3	T	A	4: 116,910,019 (GRCm39)	S185T	probably benign	Het
Entpd2	T	A	2: 25,290,921 (GRCm39)	I475N	possibly damaging	Het
Ercc2	C	A	7: 19,128,060 (GRCm39)	Q715K	probably benign	Het
Fam186b	T	C	15: 99,176,629 (GRCm39)	R754G	probably benign	Het
Fcgbp	T	A	7: 27,792,861 (GRCm39)	V955E	possibly damaging	Het
Frrs1	T	C	3: 116,689,212 (GRCm39)	V361A	possibly damaging	Het
Gabrr2	T	A	4: 33,095,284 (GRCm39)	M391K	probably benign	Het
Gm3409	T	A	5: 146,476,357 (GRCm39)	D169E	probably benign	Het
Gm4779	TCGGGGCCGGGGCCGGGGCCG	TCGGGGCCGGGGCCGGGGCCGGGGCCG	X: 100,837,777 (GRCm39)		probably benign	Het
Greb1l	C	G	18: 10,544,970 (GRCm39)	Q1433E	probably damaging	Het
Hal	T	C	10: 93,328,423 (GRCm39)	V233A	probably benign	Het
Ighv1-58	A	T	12: 115,275,915 (GRCm39)	N74K	probably benign	Het
Il12rb1	A	G	8: 71,266,343 (GRCm39)	I229M	possibly damaging	Het
Il17rd	T	C	14: 26,798,348 (GRCm39)	I56T	possibly damaging	Het
Itpr1	T	C	6: 108,518,985 (GRCm39)	V2708A	possibly damaging	Het
Klhl38	G	A	15: 58,186,376 (GRCm39)	R118W	probably damaging	Het
Lmf2	C	A	15: 89,239,733 (GRCm39)		probably benign	Het
Lrrc3b	T	C	14: 15,357,934 (GRCm38)	Y224C	probably damaging	Het
Med1	A	C	11: 98,043,634 (GRCm39)	F599C	probably benign	Het
Mrgprb4	A	G	7: 47,848,506 (GRCm39)	S141P	probably damaging	Het
Mst1r	G	T	9: 107,791,989 (GRCm39)	A842S	possibly damaging	Het
Myo3a	T	C	2: 22,436,504 (GRCm39)		probably null	Het
Nos1	A	T	5: 118,005,970 (GRCm39)	D230V	possibly damaging	Het
Nppb	T	C	4: 148,070,780 (GRCm39)	S52P	probably benign	Het
Nqo1	A	G	8: 108,119,280 (GRCm39)	I99T	probably damaging	Het
Or1j17	T	A	2: 36,578,023 (GRCm39)	M3K	probably benign	Het
Or6c2b	T	C	10: 128,947,568 (GRCm39)	H242R	probably damaging	Het
Pabir1	T	A	19: 24,454,488 (GRCm39)	H78L	probably benign	Het
Pabir1	T	A	19: 24,454,710 (GRCm39)	E4V	probably damaging	Het
Plpp7	T	G	2: 31,986,067 (GRCm39)	F82V	probably benign	Het
Podxl	G	T	6: 31,501,371 (GRCm39)	P395T	probably damaging	Het
Prr5l	T	A	2: 101,547,631 (GRCm39)	D298V	probably damaging	Het
Rad9b	A	G	5: 122,490,677 (GRCm39)	V13A	possibly damaging	Het
Rasl2-9	A	G	7: 5,128,739 (GRCm39)	W64R	probably damaging	Het
Rilp	G	T	11: 75,400,942 (GRCm39)		probably benign	Het
Ripor2	T	C	13: 24,908,984 (GRCm39)	I1034T	possibly damaging	Het
Rtn4ip1	T	C	10: 43,812,016 (GRCm39)	Y338H	probably damaging	Het
Shisa5	G	T	9: 108,883,952 (GRCm39)		probably benign	Het
Slc27a4	C	T	2: 29,702,944 (GRCm39)	T591I	probably null	Het
Snx24	G	T	18: 53,473,244 (GRCm39)	V63F	probably damaging	Het
Spata31f1e	T	C	4: 42,792,923 (GRCm39)	N403S	possibly damaging	Het
Sptbn1	A	T	11: 30,067,798 (GRCm39)	Y1805*	probably null	Het
Svep1	G	A	4: 58,046,587 (GRCm39)	Q3515*	probably null	Het
Synpo2	A	C	3: 122,907,702 (GRCm39)	M538R	probably benign	Het
Tfap2a	T	C	13: 40,874,784 (GRCm39)	K276E	probably damaging	Het
Tmem158	C	A	9: 123,089,366 (GRCm39)	S82I	probably damaging	Het
Tmtc3	G	T	10: 100,283,336 (GRCm39)	H740N	not run	Het
Top3a	A	T	11: 60,638,974 (GRCm39)	F559I	probably damaging	Het
Tysnd1	C	A	10: 61,532,328 (GRCm39)	P327T	possibly damaging	Het
Ulk4	T	A	9: 120,974,125 (GRCm39)	D969V	probably benign	Het
Vcan	T	A	13: 89,853,385 (GRCm39)	Y525F	probably benign	Het
Vmn1r127	A	G	7: 21,052,978 (GRCm39)	F270S	probably benign	Het
Vmn1r204	G	A	13: 22,740,975 (GRCm39)	S202N	probably damaging	Het
Vmn2r107	A	G	17: 20,565,878 (GRCm39)	I64M	probably benign	Het
Zfp280b	C	G	10: 75,874,537 (GRCm39)	Q139E	probably damaging	Het
Zfp322a	C	A	13: 23,541,313 (GRCm39)	G143V	probably damaging	Het
Zfp322a	C	T	13: 23,541,314 (GRCm39)	G143S	probably benign	Het
Zfyve26	A	T	12: 79,329,758 (GRCm39)	V476D	probably benign	Het
Zkscan6	A	T	11: 65,719,051 (GRCm39)	H357L	probably benign	Het

Other mutations in Pcdha3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R2497:Pcdha3	UTSW	18	37,080,556 (GRCm39)	missense	probably benign
R3702:Pcdha3	UTSW	18	37,080,401 (GRCm39)	missense	probably benign	0.16
R4090:Pcdha3	UTSW	18	37,081,504 (GRCm39)	missense	probably benign	0.04
R4273:Pcdha3	UTSW	18	37,081,144 (GRCm39)	missense	probably damaging	1.00
R4486:Pcdha3	UTSW	18	37,080,404 (GRCm39)	missense	probably damaging	1.00
R4535:Pcdha3	UTSW	18	37,081,013 (GRCm39)	missense	probably damaging	1.00
R4582:Pcdha3	UTSW	18	37,080,485 (GRCm39)	missense	probably benign
R4712:Pcdha3	UTSW	18	37,079,560 (GRCm39)	missense	probably damaging	1.00
R5160:Pcdha3	UTSW	18	37,079,480 (GRCm39)	missense	probably damaging	1.00
R5302:Pcdha3	UTSW	18	37,081,208 (GRCm39)	missense	probably damaging	0.96
R5361:Pcdha3	UTSW	18	37,079,752 (GRCm39)	missense	possibly damaging	0.80
R5535:Pcdha3	UTSW	18	37,080,989 (GRCm39)	missense	probably benign	0.02
R5682:Pcdha3	UTSW	18	37,081,040 (GRCm39)	missense	probably damaging	0.99
R6656:Pcdha3	UTSW	18	37,080,875 (GRCm39)	missense	probably benign	0.24
R6878:Pcdha3	UTSW	18	37,080,416 (GRCm39)	nonsense	probably null
R7150:Pcdha3	UTSW	18	37,080,165 (GRCm39)	missense	probably benign	0.01
R7167:Pcdha3	UTSW	18	37,080,046 (GRCm39)	missense	probably damaging	1.00
R7299:Pcdha3	UTSW	18	37,079,977 (GRCm39)	missense	possibly damaging	0.56
R7448:Pcdha3	UTSW	18	37,079,266 (GRCm39)	missense	probably benign	0.00
R7467:Pcdha3	UTSW	18	37,080,584 (GRCm39)	missense	probably damaging	1.00
R7542:Pcdha3	UTSW	18	37,080,784 (GRCm39)	missense	possibly damaging	0.86
R7659:Pcdha3	UTSW	18	37,081,219 (GRCm39)	missense	probably benign	0.14
R7761:Pcdha3	UTSW	18	37,079,347 (GRCm39)	missense	probably damaging	1.00
R7782:Pcdha3	UTSW	18	37,081,193 (GRCm39)	missense	probably damaging	0.98
R7939:Pcdha3	UTSW	18	37,080,933 (GRCm39)	missense	probably damaging	1.00
R8217:Pcdha3	UTSW	18	37,079,974 (GRCm39)	missense	probably damaging	0.99
R8440:Pcdha3	UTSW	18	37,080,914 (GRCm39)	missense	probably damaging	1.00
R8938:Pcdha3	UTSW	18	37,080,154 (GRCm39)	missense	probably benign	0.43
R9375:Pcdha3	UTSW	18	37,079,353 (GRCm39)	missense	probably benign	0.29
R9378:Pcdha3	UTSW	18	37,080,284 (GRCm39)	missense	probably damaging	1.00
R9546:Pcdha3	UTSW	18	37,079,389 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- GGAACCAATTCGTTGTTGTCTTACAG -3'
(R):5'- CCACTGATTGGGTCTAAGTGG -3'

Sequencing Primer
(F):5'- GTTGTCTTACAGTCTTAACTCAAGTG -3'
(R):5'- GGAATTTTGACAGGATTTCAAGTGAC -3'

Posted On

2019-06-26