Mutagenetix > Incidental Mutation

Incidental Mutation 'R7917:Pcdha1'

648158

Institutional Source

Beutler Lab

Gene Symbol

Pcdha1

Ensembl Gene

ENSMUSG00000103442

Gene Name

protocadherin alpha 1

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R7917 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

36930184-37187661 bp(+) (GRCm38)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 36932201 bp (GRCm38)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glutamic Acid at position 639 (D639E)

Ref Sequence

ENSEMBL: ENSMUSP00000068828 (fasta)

Gene Model

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

AlphaFold

Q91Y21

Predicted Effect

possibly damaging
Transcript: ENSMUST00000070797
AA Change: D639E

PolyPhen 2 Score 0.640 (Sensitivity: 0.87; Specificity: 0.91)

SMART Domains

Protein: ENSMUSP00000068828
Gene: ENSMUSG00000103442
AA Change: D639E

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: D639E

PolyPhen 2 Score 0.835 (Sensitivity: 0.84; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000142308
Gene: ENSMUSG00000103442
AA Change: D639E

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: 99.6%
20x: 98.7%

Validation Efficiency

97% (36/37)

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: 40 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca8a	G	T	11: 110,068,107	H730Q	probably damaging	Het
Adam20	A	G	8: 40,796,371	D506G	probably damaging	Het
Brinp1	A	G	4: 68,904,953	M1T	probably null	Het
Ccnc	T	A	4: 21,748,158	N273K	possibly damaging	Het
Cfdp1	C	A	8: 111,840,401	V159L	possibly damaging	Het
Cyb5r1	T	A	1: 134,406,900		probably benign	Het
Dsp	C	T	13: 38,167,639	Q145*	probably null	Het
Exosc9	G	A	3: 36,553,819	V59I	probably damaging	Het
Fermt2	C	G	14: 45,461,861	R592T	probably damaging	Het
Fryl	A	G	5: 73,054,532	S2381P	probably damaging	Het
Fscn2	G	A	11: 120,367,256	E335K	possibly damaging	Het
Hapln1	T	C	13: 89,607,878	I267T	probably benign	Het
Hdac9	T	A	12: 34,433,210	I93L	probably benign	Het
Igfn1	T	C	1: 135,971,968	D535G	probably damaging	Het
Ighv1-4	A	T	12: 114,487,545	F9I	possibly damaging	Het
Il3ra	T	A	14: 14,350,773	H262Q	possibly damaging	Het
Kti12	A	C	4: 108,848,246	E119A	probably benign	Het
Kti12	G	T	4: 108,848,247	E119D	probably benign	Het
Mtg1	A	T	7: 140,147,265	D227V	probably damaging	Het
Nrcam	T	G	12: 44,573,763		probably null	Het
Olfr1308	A	C	2: 111,960,965	V36G	probably damaging	Het
Olfr309	T	C	7: 86,306,478	T212A	probably damaging	Het
Olfr906	T	A	9: 38,488,609	Y193*	probably null	Het
Pcdhga8	T	A	18: 37,727,616	V575E	possibly damaging	Het
Pcif1	G	T	2: 164,888,472	R375L	probably benign	Het
Pcna	A	T	2: 132,253,009	S10T	probably benign	Het
Pdzd8	A	G	19: 59,345,086	S168P	probably damaging	Het
Pkd1l3	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	GACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCAACAAACATGACATCAGACACACCTGCATCCAGCAGCCCA	8: 109,624,195		probably benign	Het
Polq	T	A	16: 37,065,288	D1842E	probably benign	Het
Rag2	A	T	2: 101,629,695	N117Y	probably damaging	Het
Scnn1g	T	C	7: 121,743,693	Y290H	probably damaging	Het
Sri	T	C	5: 8,063,409		probably null	Het
Tek	T	C	4: 94,820,135	V361A	possibly damaging	Het
Terf1	T	A	1: 15,819,076	L243Q	probably damaging	Het
Thrap3	G	A	4: 126,175,420	T646I	probably damaging	Het
Uba1y	A	G	Y: 821,274	I86V	probably benign	Het
Vmn2r29	A	G	7: 7,231,728	S720P	probably damaging	Het
Zeb2	T	C	2: 44,996,409	N879D	possibly damaging	Het
Zfp266	T	C	9: 20,505,127	T56A	probably benign	Het
Zxdc	T	A	6: 90,382,009	I541N	probably damaging	Het

Other mutations in Pcdha1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdha1	APN	18	36932175	missense	probably damaging	0.99
R0062:Pcdha1	UTSW	18	37006628	missense	probably benign	0.08
R0108:Pcdha1	UTSW	18	36998756	missense	probably benign
R0543:Pcdha1	UTSW	18	37185068	missense	probably damaging	1.00
R1599:Pcdha1	UTSW	18	37185237	missense	probably damaging	1.00
R1717:Pcdha1	UTSW	18	36932184	missense	probably benign	0.01
R2301:Pcdha1	UTSW	18	37156183	missense	probably damaging	1.00
R3038:Pcdha1	UTSW	18	36931011	missense	probably damaging	1.00
R3086:Pcdha1	UTSW	18	36930948	missense	possibly damaging	0.95
R3693:Pcdha1	UTSW	18	36932308	missense	possibly damaging	0.95
R3783:Pcdha1	UTSW	18	36930802	missense	probably damaging	1.00
R3881:Pcdha1	UTSW	18	36931401	missense	possibly damaging	0.91
R4012:Pcdha1	UTSW	18	36931136	missense	probably benign	0.02
R4540:Pcdha1	UTSW	18	36931627	missense	probably damaging	1.00
R4597:Pcdha1	UTSW	18	36931906	missense	possibly damaging	0.64
R4678:Pcdha1	UTSW	18	36930912	missense	probably benign	0.00
R4998:Pcdha1	UTSW	18	36932416	missense	probably damaging	1.00
R5466:Pcdha1	UTSW	18	36932259	missense	possibly damaging	0.73
R5518:Pcdha1	UTSW	18	36932362	missense	probably benign	0.23
R5673:Pcdha1	UTSW	18	36930673	missense	probably damaging	1.00
R5925:Pcdha1	UTSW	18	36930671	missense	probably damaging	1.00
R5942:Pcdha1	UTSW	18	36930391	missense	probably damaging	1.00
R5963:Pcdha1	UTSW	18	36931171	missense	probably damaging	0.99
R6034:Pcdha1	UTSW	18	36930598	missense	probably damaging	1.00
R6034:Pcdha1	UTSW	18	36930598	missense	probably damaging	1.00
R6107:Pcdha1	UTSW	18	36932301	missense	probably benign	0.00
R6329:Pcdha1	UTSW	18	36932248	missense	probably damaging	1.00
R6479:Pcdha1	UTSW	18	36931456	missense	probably benign	0.28
R6503:Pcdha1	UTSW	18	36931671	missense	probably damaging	1.00
R6907:Pcdha1	UTSW	18	36931071	missense	probably benign	0.01
R7011:Pcdha1	UTSW	18	36930535	missense	probably damaging	1.00
R7030:Pcdha1	UTSW	18	37159273	missense	probably damaging	0.97
R7314:Pcdha1	UTSW	18	36931500	missense	probably damaging	0.99
R7343:Pcdha1	UTSW	18	36930649	missense	probably damaging	1.00
R7699:Pcdha1	UTSW	18	36931062	missense	probably damaging	0.98
R7700:Pcdha1	UTSW	18	36931062	missense	probably damaging	0.98
R7768:Pcdha1	UTSW	18	36932167	missense	probably damaging	1.00
R7780:Pcdha1	UTSW	18	36932458	missense	probably benign	0.28
R7800:Pcdha1	UTSW	18	36931373	missense	probably damaging	1.00
R8325:Pcdha1	UTSW	18	36930814	missense	possibly damaging	0.47
R8699:Pcdha1	UTSW	18	36931023	missense	probably benign	0.00
R9400:Pcdha1	UTSW	18	36931707	missense	probably benign	0.43
R9513:Pcdha1	UTSW	18	36932233	missense	probably benign	0.26
R9746:Pcdha1	UTSW	18	36932660	missense	probably benign

Predicted Primers

PCR Primer
(F):5'- AACTGGTGTCACGGACAATGG -3'
(R):5'- TGAGCACTAACAGGCTGGAC -3'

Sequencing Primer
(F):5'- TCACGGACAATGGGTGCAG -3'
(R):5'- GATGATCAGGTACACGTTGACATCC -3'

Posted On

2020-09-15