Mutagenetix > Incidental Mutation

Incidental Mutation 'R9608:Pcdh1'

724061

Institutional Source

Beutler Lab

Gene Symbol

Pcdh1

Ensembl Gene

ENSMUSG00000051375

Gene Name

protocadherin 1

Synonyms

2010005A06Rik

MMRRC Submission

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.365) question?

Stock #

R9608 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

38318967-38345023 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 38330904 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Methionine at position 839 (V839M)

Ref Sequence

ENSEMBL: ENSMUSP00000055199 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000057185] [ENSMUST00000159405] [ENSMUST00000160721] [ENSMUST00000161701]

AlphaFold

Q8CFX3

Predicted Effect

possibly damaging
Transcript: ENSMUST00000057185
AA Change: V839M

PolyPhen 2 Score 0.910 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000055199
Gene: ENSMUSG00000051375
AA Change: V839M

Domain	Start	End	E-Value	Type
signal peptide	1	33	N/A	INTRINSIC
Pfam:Cadherin_2	36	120	2e-8	PFAM
CA	168	256	5.18e-18	SMART
CA	280	363	5.68e-24	SMART
CA	395	482	1.84e-23	SMART
CA	506	588	2.99e-32	SMART
CA	612	691	9.36e-25	SMART
CA	717	798	9.9e-15	SMART
transmembrane domain	830	852	N/A	INTRINSIC
low complexity region	876	903	N/A	INTRINSIC
low complexity region	951	964	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000159405
AA Change: V839M

PolyPhen 2 Score 0.910 (Sensitivity: 0.81; Specificity: 0.94)

SMART Domains

Protein: ENSMUSP00000125309
Gene: ENSMUSG00000051375
AA Change: V839M

Domain	Start	End	E-Value	Type
signal peptide	1	33	N/A	INTRINSIC
Pfam:Cadherin_2	36	120	2e-8	PFAM
CA	168	256	5.18e-18	SMART
CA	280	363	5.68e-24	SMART
CA	395	482	1.84e-23	SMART
CA	506	588	2.99e-32	SMART
CA	612	691	9.36e-25	SMART
CA	717	798	9.9e-15	SMART
transmembrane domain	830	852	N/A	INTRINSIC
low complexity region	876	903	N/A	INTRINSIC
low complexity region	951	964	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000160721

SMART Domains

Protein: ENSMUSP00000124732
Gene: ENSMUSG00000051375

Domain	Start	End	E-Value	Type
signal peptide	1	33	N/A	INTRINSIC
Pfam:Cadherin_2	36	120	9.9e-10	PFAM
CA	168	256	5.18e-18	SMART
low complexity region	310	321	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000161701
AA Change: V700M

PolyPhen 2 Score 0.949 (Sensitivity: 0.79; Specificity: 0.95)

SMART Domains

Protein: ENSMUSP00000125576
Gene: ENSMUSG00000051375
AA Change: V700M

Domain	Start	End	E-Value	Type
CA	29	117	5.18e-18	SMART
CA	141	224	5.68e-24	SMART
CA	256	343	1.84e-23	SMART
CA	367	449	2.99e-32	SMART
CA	473	552	9.36e-25	SMART
CA	578	659	9.9e-15	SMART
transmembrane domain	691	713	N/A	INTRINSIC
low complexity region	737	764	N/A	INTRINSIC
low complexity region	812	825	N/A	INTRINSIC
low complexity region	903	914	N/A	INTRINSIC
low complexity region	1029	1040	N/A	INTRINSIC
low complexity region	1059	1071	N/A	INTRINSIC

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.9%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the protocadherin subfamily within the cadherin superfamily. The encoded protein is a membrane protein found at cell-cell boundaries. It is involved in neural cell adhesion, suggesting a possible role in neuronal development. The protein includes an extracelllular region, containing 7 cadherin-like domains, a transmembrane region and a C-terminal cytoplasmic region. Cells expressing the protein showed cell aggregation activity. Alternative splicing occurs in this gene. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 86 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Acsl5	T	A	19: 55,272,884 (GRCm39)	I333N	probably damaging	Het
Adam2	T	C	14: 66,291,279 (GRCm39)	N333S	probably null	Het
Adgrb2	A	G	4: 129,907,352 (GRCm39)	T955A	probably damaging	Het
Agxt2	T	C	15: 10,400,624 (GRCm39)	F476S	possibly damaging	Het
Asb14	T	A	14: 26,634,148 (GRCm39)	F451Y	probably damaging	Het
Atg9a	A	T	1: 75,161,739 (GRCm39)	N602K	possibly damaging	Het
Atp2a3	T	C	11: 72,879,866 (GRCm39)	I978T	probably benign	Het
BC034090	A	G	1: 155,099,135 (GRCm39)	V550A	possibly damaging	Het
Bud23	T	A	5: 135,086,526 (GRCm39)		probably null	Het
C1qtnf3	A	T	15: 10,952,568 (GRCm39)	H10L	probably benign	Het
Cage1	G	C	13: 38,195,371 (GRCm39)	I783M	possibly damaging	Het
Ccdc142	C	T	6: 83,084,082 (GRCm39)	Q496*	probably null	Het
Cd163	A	C	6: 124,286,163 (GRCm39)	K238Q	possibly damaging	Het
Cdh6	A	T	15: 13,064,621 (GRCm39)	Y90N	probably damaging	Het
Cpeb1	A	G	7: 81,021,758 (GRCm39)		probably null	Het
Cpt2	G	T	4: 107,765,341 (GRCm39)	P141Q	probably damaging	Het
Cspg4	T	A	9: 56,792,836 (GRCm39)	H190Q	probably benign	Het
Dcst1	T	C	3: 89,266,442 (GRCm39)	M139V	possibly damaging	Het
Dennd5a	G	C	7: 109,520,713 (GRCm39)	N381K	probably damaging	Het
Dera	A	G	6: 137,813,876 (GRCm39)	R299G	possibly damaging	Het
Dnah2	C	T	11: 69,344,888 (GRCm39)	G2729R	probably null	Het
Dnajc11	A	G	4: 152,034,978 (GRCm39)	E67G	possibly damaging	Het
Eif2ak3	T	A	6: 70,841,511 (GRCm39)	C152*	probably null	Het
Eln	T	G	5: 134,755,331 (GRCm39)	K241Q	unknown	Het
Exoc6b	C	T	6: 84,602,106 (GRCm39)		probably null	Het
Eya1	A	T	1: 14,373,029 (GRCm39)	I30K	probably benign	Het
Fbxo39	A	G	11: 72,208,101 (GRCm39)	K151R	probably benign	Het
Fer	A	G	17: 64,214,327 (GRCm39)	T87A	probably benign	Het
Fgf4	A	T	7: 144,415,335 (GRCm39)	N32Y	possibly damaging	Het
Fkbp6	G	A	5: 135,375,027 (GRCm39)	P129S	probably damaging	Het
Fndc7	C	A	3: 108,774,597 (GRCm39)	V554F	probably damaging	Het
Frk	G	A	10: 34,481,873 (GRCm39)		probably null	Het
Ghrhr	T	A	6: 55,357,786 (GRCm39)	I139N	possibly damaging	Het
Gm17175	A	T	14: 51,809,099 (GRCm39)	M89K	probably damaging	Het
Gm4787	A	T	12: 81,425,086 (GRCm39)	N357K	probably benign	Het
Gpihbp1	G	A	15: 75,469,612 (GRCm39)	C109Y	probably damaging	Het
Gps1	T	C	11: 120,677,641 (GRCm39)	V257A	probably benign	Het
H2-M3	T	C	17: 37,581,159 (GRCm39)	S3P	probably benign	Het
Hmcn1	G	A	1: 150,475,303 (GRCm39)	P4674L	probably damaging	Het
Hoxa11	T	C	6: 52,222,224 (GRCm39)	D159G	probably benign	Het
Kcnn4	G	A	7: 24,083,503 (GRCm39)	D395N	probably damaging	Het
Krt222	T	C	11: 99,126,981 (GRCm39)	E213G	probably damaging	Het
Lmcd1	A	G	6: 112,306,785 (GRCm39)	D319G	possibly damaging	Het
Ltv1	A	G	10: 13,066,440 (GRCm39)	F62S	probably damaging	Het
Man2a1	G	T	17: 65,041,953 (GRCm39)	R957L	probably damaging	Het
Mcm5	C	T	8: 75,844,168 (GRCm39)	S313F	probably benign	Het
Mrpl45	T	G	11: 97,217,687 (GRCm39)	V197G	probably damaging	Het
Ndn	C	T	7: 61,998,337 (GRCm39)	P61L	possibly damaging	Het
Nek4	T	C	14: 30,675,904 (GRCm39)	Y73H	probably damaging	Het
Nom1	T	A	5: 29,642,750 (GRCm39)	V417D	probably damaging	Het
Or10q1b	A	T	19: 13,682,868 (GRCm39)	I226F	probably damaging	Het
Or4k5	A	G	14: 50,386,055 (GRCm39)	I92T	probably benign	Het
Or5p68	A	G	7: 107,945,513 (GRCm39)	L225P	probably damaging	Het
Pacs1	A	G	19: 5,193,862 (GRCm39)	S556P	probably damaging	Het
Pcdhb18	T	A	18: 37,623,694 (GRCm39)	N341K	probably damaging	Het
Pde6d	G	A	1: 86,473,424 (GRCm39)	T124M	possibly damaging	Het
Piezo2	T	A	18: 63,280,016 (GRCm39)	E185V	probably benign	Het
Pkhd1l1	T	C	15: 44,442,029 (GRCm39)	V3656A	possibly damaging	Het
Plcg1	A	G	2: 160,597,671 (GRCm39)	Y771C	probably benign	Het
Ppdpf	T	C	2: 180,829,668 (GRCm39)	L41P	probably benign	Het
Prepl	T	C	17: 85,376,321 (GRCm39)	T578A	probably benign	Het
Prkdc	C	A	16: 15,548,334 (GRCm39)	L1981M	possibly damaging	Het
Prkdc	T	A	16: 15,548,335 (GRCm39)	L1981Q	probably damaging	Het
Rb1cc1	C	T	1: 6,318,528 (GRCm39)	S649L	probably benign	Het
Rbbp6	A	G	7: 122,591,268 (GRCm39)	T457A	possibly damaging	Het
Sbf1	T	A	15: 89,191,808 (GRCm39)		probably null	Het
Scn1a	T	C	2: 66,152,687 (GRCm39)	I776V	probably benign	Het
Sec23a	G	A	12: 59,019,804 (GRCm39)	P588S	probably benign	Het
Slfn5	A	G	11: 82,851,830 (GRCm39)	D652G	possibly damaging	Het
Slfn5	C	A	11: 82,852,321 (GRCm39)	P816T	probably benign	Het
Smarcad1	C	T	6: 65,091,318 (GRCm39)	T1013I	probably damaging	Het
Spidr	G	A	16: 15,855,474 (GRCm39)	T347I	probably benign	Het
Stx1b	A	T	7: 127,406,551 (GRCm39)	M266K	probably damaging	Het
Tarm1	A	G	7: 3,551,062 (GRCm39)		probably benign	Het
Tfap2c	A	T	2: 172,391,764 (GRCm39)	K4*	probably null	Het
Trpm5	A	T	7: 142,633,148 (GRCm39)	V819E	possibly damaging	Het
Trrap	A	G	5: 144,780,128 (GRCm39)	T3240A	possibly damaging	Het
Uqcc2	A	T	17: 27,341,709 (GRCm39)	V130D	probably benign	Het
Uspl1	T	A	5: 149,151,870 (GRCm39)	D1023E	probably benign	Het
Vinac1	C	T	2: 128,878,550 (GRCm39)	W1125*	probably null	Het
Vmn2r28	A	T	7: 5,491,220 (GRCm39)	H342Q	probably benign	Het
Vmn2r33	A	T	7: 7,557,153 (GRCm39)	C516S	possibly damaging	Het
Vps45	G	A	3: 95,940,982 (GRCm39)	R420W	probably damaging	Het
Zfp42	C	T	8: 43,749,172 (GRCm39)	V110I	possibly damaging	Het
Zfp467	T	A	6: 48,404,776 (GRCm39)	K100N	unknown	Het
Zfyve16	A	T	13: 92,636,788 (GRCm39)	S1307R	probably damaging	Het

Other mutations in Pcdh1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00714:Pcdh1	APN	18	38,331,782 (GRCm39)	missense	possibly damaging	0.65
IGL00919:Pcdh1	APN	18	38,335,865 (GRCm39)	nonsense	probably null
IGL01744:Pcdh1	APN	18	38,336,302 (GRCm39)	missense	probably damaging	1.00
PIT4260001:Pcdh1	UTSW	18	38,336,419 (GRCm39)	missense	probably damaging	0.99
R0542:Pcdh1	UTSW	18	38,322,975 (GRCm39)	missense	probably damaging	0.99
R1449:Pcdh1	UTSW	18	38,322,929 (GRCm39)	missense	probably damaging	0.99
R1540:Pcdh1	UTSW	18	38,322,779 (GRCm39)	missense	probably benign	0.01
R1642:Pcdh1	UTSW	18	38,332,283 (GRCm39)	missense	possibly damaging	0.84
R1672:Pcdh1	UTSW	18	38,325,233 (GRCm39)	missense	probably damaging	1.00
R1695:Pcdh1	UTSW	18	38,335,921 (GRCm39)	missense	probably damaging	1.00
R1727:Pcdh1	UTSW	18	38,336,085 (GRCm39)	nonsense	probably null
R1781:Pcdh1	UTSW	18	38,322,977 (GRCm39)	missense	probably damaging	1.00
R1793:Pcdh1	UTSW	18	38,331,938 (GRCm39)	missense	probably damaging	0.99
R1839:Pcdh1	UTSW	18	38,332,538 (GRCm39)	missense	possibly damaging	0.82
R1843:Pcdh1	UTSW	18	38,325,278 (GRCm39)	splice site	probably null
R1882:Pcdh1	UTSW	18	38,335,895 (GRCm39)	missense	possibly damaging	0.49
R2261:Pcdh1	UTSW	18	38,331,710 (GRCm39)	missense	probably benign	0.01
R2262:Pcdh1	UTSW	18	38,331,710 (GRCm39)	missense	probably benign	0.01
R2263:Pcdh1	UTSW	18	38,331,710 (GRCm39)	missense	probably benign	0.01
R2511:Pcdh1	UTSW	18	38,332,532 (GRCm39)	missense	possibly damaging	0.95
R2937:Pcdh1	UTSW	18	38,322,815 (GRCm39)	missense	probably benign	0.40
R3941:Pcdh1	UTSW	18	38,332,511 (GRCm39)	missense	probably benign	0.02
R3942:Pcdh1	UTSW	18	38,332,511 (GRCm39)	missense	probably benign	0.02
R4057:Pcdh1	UTSW	18	38,331,950 (GRCm39)	missense	probably damaging	0.98
R4155:Pcdh1	UTSW	18	38,336,159 (GRCm39)	missense	probably damaging	0.99
R4169:Pcdh1	UTSW	18	38,331,358 (GRCm39)	missense	probably damaging	1.00
R4617:Pcdh1	UTSW	18	38,330,913 (GRCm39)	missense	probably benign	0.00
R4690:Pcdh1	UTSW	18	38,336,528 (GRCm39)	missense	probably benign	0.33
R4825:Pcdh1	UTSW	18	38,322,912 (GRCm39)	missense	possibly damaging	0.77
R5201:Pcdh1	UTSW	18	38,331,971 (GRCm39)	missense	probably damaging	0.98
R5266:Pcdh1	UTSW	18	38,325,252 (GRCm39)	missense	probably damaging	1.00
R5267:Pcdh1	UTSW	18	38,325,252 (GRCm39)	missense	probably damaging	1.00
R5351:Pcdh1	UTSW	18	38,330,819 (GRCm39)	missense	probably damaging	1.00
R5568:Pcdh1	UTSW	18	38,330,420 (GRCm39)	missense	probably damaging	1.00
R5729:Pcdh1	UTSW	18	38,335,999 (GRCm39)	missense	probably damaging	1.00
R5731:Pcdh1	UTSW	18	38,331,651 (GRCm39)	missense	probably damaging	1.00
R6043:Pcdh1	UTSW	18	38,336,327 (GRCm39)	missense	probably damaging	0.97
R6278:Pcdh1	UTSW	18	38,332,263 (GRCm39)	missense	probably benign	0.29
R6333:Pcdh1	UTSW	18	38,331,860 (GRCm39)	missense	probably benign	0.25
R6498:Pcdh1	UTSW	18	38,330,490 (GRCm39)	missense	probably benign	0.18
R6937:Pcdh1	UTSW	18	38,336,528 (GRCm39)	missense	possibly damaging	0.86
R6994:Pcdh1	UTSW	18	38,331,553 (GRCm39)	missense	probably damaging	1.00
R7242:Pcdh1	UTSW	18	38,336,270 (GRCm39)	missense	probably benign	0.06
R7289:Pcdh1	UTSW	18	38,322,966 (GRCm39)	missense	probably damaging	0.99
R7391:Pcdh1	UTSW	18	38,335,838 (GRCm39)	missense	possibly damaging	0.95
R7702:Pcdh1	UTSW	18	38,336,569 (GRCm39)	missense	unknown
R7738:Pcdh1	UTSW	18	38,330,529 (GRCm39)	missense	probably benign	0.02
R7849:Pcdh1	UTSW	18	38,322,662 (GRCm39)	missense	probably benign	0.01
R7941:Pcdh1	UTSW	18	38,332,133 (GRCm39)	missense	probably damaging	1.00
R8109:Pcdh1	UTSW	18	38,332,049 (GRCm39)	missense	probably damaging	1.00
R8675:Pcdh1	UTSW	18	38,332,229 (GRCm39)	missense	probably damaging	1.00
R8851:Pcdh1	UTSW	18	38,325,155 (GRCm39)	missense	probably damaging	1.00
R8947:Pcdh1	UTSW	18	38,332,073 (GRCm39)	missense	possibly damaging	0.89
R9443:Pcdh1	UTSW	18	38,330,633 (GRCm39)	missense	probably damaging	1.00
R9448:Pcdh1	UTSW	18	38,330,492 (GRCm39)	missense	probably damaging	1.00
X0027:Pcdh1	UTSW	18	38,322,841 (GRCm39)	nonsense	probably null
Z1088:Pcdh1	UTSW	18	38,331,120 (GRCm39)	missense	probably damaging	1.00
Z1176:Pcdh1	UTSW	18	38,331,741 (GRCm39)	missense	possibly damaging	0.79

Predicted Primers

PCR Primer
(F):5'- ACTGGCTTCACAGGTTTCGG -3'
(R):5'- TCGTGGTGAAGGTCAGTGAC -3'

Sequencing Primer
(F):5'- CACAGGTTTCGGTGACTTGC -3'
(R):5'- TCAGTGACCGTGGCAAGC -3'

Posted On

2022-09-12