Mutagenetix > Incidental Mutation

Incidental Mutation 'R9483:Pcdhga4'

716404

Institutional Source

Beutler Lab

Gene Symbol

Pcdhga4

Ensembl Gene

ENSMUSG00000103677

Gene Name

protocadherin gamma subfamily A, 4

Synonyms

MMRRC Submission

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.123) question?

Stock #

R9483 (G1)

Quality Score

225.009

Status

Not validated

Chromosome

Chromosomal Location

37818290-37974923 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to A at 37819746 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Serine to Threonine at position 432 (S432T)

Ref Sequence

ENSEMBL: ENSMUSP00000142140 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000073447] [ENSMUST00000115661] [ENSMUST00000192931] [ENSMUST00000193869] [ENSMUST00000194190] [ENSMUST00000194418] [ENSMUST00000194544] [ENSMUST00000195112]

AlphaFold

Q91XY4

Predicted Effect

probably benign
Transcript: ENSMUST00000073447

SMART Domains

Protein: ENSMUSP00000073150
Gene: ENSMUSG00000104346

Domain	Start	End	E-Value	Type
signal peptide	1	22	N/A	INTRINSIC
CA	42	128	2.15e-2	SMART
CA	152	237	4.8e-13	SMART
CA	261	342	9.36e-25	SMART
CA	366	447	6.62e-25	SMART
CA	471	557	6.72e-26	SMART
CA	588	666	2.15e-15	SMART
Pfam:Cadherin_C_2	685	768	4.8e-24	PFAM
Pfam:Cadherin_tail	805	928	8.1e-38	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000115661

SMART Domains

Protein: ENSMUSP00000111325
Gene: ENSMUSG00000103458

Domain	Start	End	E-Value	Type
CA	20	131	5.3e-2	SMART
CA	155	240	1.51e-19	SMART
CA	264	348	7.6e-25	SMART
CA	372	453	1.42e-24	SMART
CA	477	563	1.42e-24	SMART
CA	594	674	4.12e-12	SMART
low complexity region	706	721	N/A	INTRINSIC
Pfam:Cadherin_tail	796	930	3.9e-58	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000192931

SMART Domains

Protein: ENSMUSP00000141348
Gene: ENSMUSG00000103037

Domain	Start	End	E-Value	Type
CA	36	119	8e-3	SMART
CA	143	228	1.34e-20	SMART
CA	252	333	1.52e-24	SMART
CA	357	438	9.22e-24	SMART
CA	462	548	1.24e-24	SMART
CA	579	660	1.3e-9	SMART
transmembrane domain	679	701	N/A	INTRINSIC
low complexity region	899	918	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193869

SMART Domains

Protein: ENSMUSP00000141482
Gene: ENSMUSG00000103332

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	45	131	1.64e-2	SMART
CA	155	240	6.42e-23	SMART
CA	264	345	1.76e-20	SMART
CA	369	450	2.27e-23	SMART
CA	474	560	1.5e-23	SMART
CA	591	669	1.17e-16	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	912	931	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000193984

Predicted Effect

probably benign
Transcript: ENSMUST00000194190

SMART Domains

Protein: ENSMUSP00000142062
Gene: ENSMUSG00000103144

Domain	Start	End	E-Value	Type
signal peptide	1	28	N/A	INTRINSIC
CA	31	131	3.16e-2	SMART
CA	155	240	5.39e-16	SMART
CA	264	345	6.72e-26	SMART
CA	369	450	1.32e-24	SMART
CA	474	560	4.17e-22	SMART
CA	591	669	4.48e-13	SMART
transmembrane domain	692	714	N/A	INTRINSIC
low complexity region	912	931	N/A	INTRINSIC

Predicted Effect

possibly damaging
Transcript: ENSMUST00000194418
AA Change: S432T

PolyPhen 2 Score 0.733 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000142140
Gene: ENSMUSG00000103677
AA Change: S432T

Domain	Start	End	E-Value	Type
CA	44	130	1.64e-2	SMART
CA	154	239	3.93e-18	SMART
CA	263	344	5.22e-23	SMART
CA	368	449	5.02e-25	SMART
CA	473	559	2.07e-26	SMART
CA	590	668	6.84e-18	SMART
transmembrane domain	690	712	N/A	INTRINSIC
low complexity region	911	930	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000194544

SMART Domains

Protein: ENSMUSP00000141847
Gene: ENSMUSG00000102836

Domain	Start	End	E-Value	Type
Blast:CA	18	66	5e-20	BLAST

Predicted Effect

probably benign
Transcript: ENSMUST00000195112

SMART Domains

Protein: ENSMUSP00000141449
Gene: ENSMUSG00000102748

Domain	Start	End	E-Value	Type
CA	24	130	8.18e-3	SMART
CA	154	239	1.39e-18	SMART
CA	263	344	7.91e-23	SMART
CA	368	449	2.27e-23	SMART
CA	473	559	1.24e-24	SMART
CA	590	671	1.3e-9	SMART
transmembrane domain	690	712	N/A	INTRINSIC
low complexity region	909	928	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000195163

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.5%
20x: 98.2%

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 gamma gene cluster, one of three related clusters tandemly linked on chromosome five. These gene clusters have an immunoglobulin-like organization, suggesting that a novel mechanism may be involved in their regulation and expression. The gamma gene cluster includes 22 genes divided into 3 subfamilies. Subfamily A contains 12 genes, subfamily B contains 7 genes and 2 pseudogenes, and the more distantly related subfamily C contains 3 genes. The tandem array of 22 large, variable region exons are followed by a constant region, containing 3 exons shared by all genes in the cluster. Each variable region exon encodes the extracellular region, which includes 6 cadherin ectodomains and a transmembrane region. The constant region exons encode the common cytoplasmic region. These neural cadherin-like cell adhesion proteins most likely play a critical role in the establishment and function of specific cell-cell connections in the brain. Alternative splicing has been described for the gamma cluster genes. [provided by RefSeq, Jul 2008]

Allele List at MGI

Other mutations in this stock

Total: 77 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
2900026A02Rik	A	T	5: 113,339,010 (GRCm39)	M334K	probably benign	Het
Abca1	A	T	4: 53,060,351 (GRCm39)	I1525N	probably benign	Het
Abca4	A	T	3: 121,879,275 (GRCm39)	I398F		Het
Acbd3	A	G	1: 180,572,721 (GRCm39)	D327G	probably benign	Het
Acsm3	A	G	7: 119,383,166 (GRCm39)	T544A	probably damaging	Het
Atp11a	C	T	8: 12,901,087 (GRCm39)	T972M	probably damaging	Het
Cbfb	C	T	8: 105,929,123 (GRCm39)	R147*	probably null	Het
Ccdc17	G	T	4: 116,454,144 (GRCm39)	R54L	probably benign	Het
Cracdl	T	G	1: 37,670,496 (GRCm39)	E148A	probably damaging	Het
Cuedc2	G	T	19: 46,319,399 (GRCm39)	A223E	probably benign	Het
Cul5	T	C	9: 53,532,474 (GRCm39)	I787V	probably benign	Het
D430041D05Rik	T	A	2: 104,087,563 (GRCm39)	H471L	probably benign	Het
Ddx39a	T	C	8: 84,448,916 (GRCm39)	Y264H	probably benign	Het
Dlgap3	C	A	4: 127,127,665 (GRCm39)	R778S	probably damaging	Het
Esrrg	T	C	1: 187,930,848 (GRCm39)	V313A	probably damaging	Het
Fam124a	T	C	14: 62,844,100 (GRCm39)	I536T	probably damaging	Het
Fbxo21	T	C	5: 118,127,272 (GRCm39)	F275L	possibly damaging	Het
Gabrg1	C	A	5: 70,999,558 (GRCm39)	G2V	possibly damaging	Het
Gcc1	G	T	6: 28,418,089 (GRCm39)	A748D	probably damaging	Het
Gjb6	T	C	14: 57,361,511 (GRCm39)	D250G	probably benign	Het
Gm44501	A	T	17: 40,889,872 (GRCm39)	K129*	probably null	Het
Hmcn2	T	G	2: 31,320,375 (GRCm39)	L3952R		Het
Hpd	A	G	5: 123,312,535 (GRCm39)	I278T	probably damaging	Het
Igsf3	T	A	3: 101,346,904 (GRCm39)	F613Y	probably damaging	Het
Igsf3	T	C	3: 101,346,817 (GRCm39)	F584S	probably damaging	Het
Ik	A	G	18: 36,886,635 (GRCm39)	D369G	probably benign	Het
Ikbke	A	G	1: 131,198,719 (GRCm39)	L365P	probably damaging	Het
Il22ra2	A	T	10: 19,508,542 (GRCm39)	Q190L	possibly damaging	Het
Itga6	T	C	2: 71,679,834 (GRCm39)	V1033A	probably benign	Het
Kif18a	T	C	2: 109,120,032 (GRCm39)	Y112H	probably damaging	Het
Krt75	T	C	15: 101,482,238 (GRCm39)	H10R	probably benign	Het
L3mbtl1	T	A	2: 162,790,734 (GRCm39)	L93H	probably benign	Het
Lrfn1	G	A	7: 28,158,183 (GRCm39)	C34Y	probably damaging	Het
Lrrc47	A	T	4: 154,101,920 (GRCm39)	I396F	probably damaging	Het
Mgat3	T	A	15: 80,095,641 (GRCm39)	V156E	probably benign	Het
Mtus2	A	G	5: 148,232,300 (GRCm39)	D1120G	possibly damaging	Het
Muc5ac	G	T	7: 141,365,465 (GRCm39)	E2700*	probably null	Het
Nxpe5	A	T	5: 138,228,591 (GRCm39)		probably benign	Het
Or51v15-ps1	T	C	7: 103,278,931 (GRCm39)	T79A	probably damaging	Het
Or5aq6	A	T	2: 86,923,390 (GRCm39)	M117K	possibly damaging	Het
Pdk4	T	A	6: 5,486,716 (GRCm39)	M353L	probably benign	Het
Ppp1r13b	T	A	12: 111,800,210 (GRCm39)	K645N	probably benign	Het
Ppt1	A	T	4: 122,751,367 (GRCm39)	D288V	possibly damaging	Het
Prkcb	A	G	7: 122,181,663 (GRCm39)	Y417C	probably damaging	Het
Prss22	A	G	17: 24,215,721 (GRCm39)	I67T	probably damaging	Het
Rab29	T	C	1: 131,795,508 (GRCm39)	V40A	possibly damaging	Het
Rae1	T	C	2: 172,849,941 (GRCm39)		probably null	Het
Rasa3	C	T	8: 13,630,033 (GRCm39)		probably null	Het
Rasgrp3	A	G	17: 75,807,717 (GRCm39)	D258G	probably benign	Het
Rcc1	T	A	4: 132,062,808 (GRCm39)	T208S	probably benign	Het
Rgs3	C	A	4: 62,575,354 (GRCm39)	Y580*	probably null	Het
Rpe65	C	T	3: 159,328,318 (GRCm39)	P405S	probably damaging	Het
Rsf1	GGCGGC	GGCGGCGGCAGCGGC	7: 97,229,137 (GRCm39)		probably benign	Het
Rsph4a	A	G	10: 33,790,418 (GRCm39)	E669G	probably damaging	Het
Rusc1	A	T	3: 88,994,113 (GRCm39)	V964E	probably benign	Het
Rusc2	A	G	4: 43,415,897 (GRCm39)	N401S	probably damaging	Het
Slc10a1	G	T	12: 81,002,864 (GRCm39)	T258K	probably damaging	Het
Slc5a9	A	G	4: 111,747,418 (GRCm39)	L323P	probably damaging	Het
Slc6a17	T	A	3: 107,378,772 (GRCm39)	I637F	possibly damaging	Het
Slc8a2	A	G	7: 15,886,780 (GRCm39)	E641G	possibly damaging	Het
Sptbn2	G	T	19: 4,789,974 (GRCm39)	A1321S	probably damaging	Het
Ssh2	G	T	11: 77,283,976 (GRCm39)	A77S	possibly damaging	Het
St13	G	T	15: 81,250,587 (GRCm39)	N316K	probably damaging	Het
Taf10	A	G	7: 105,393,062 (GRCm39)	M121T	probably benign	Het
Tcta	T	C	9: 108,182,942 (GRCm39)	T68A	probably damaging	Het
Timd2	A	T	11: 46,577,889 (GRCm39)	Y81N	probably damaging	Het
Tln2	T	C	9: 67,299,769 (GRCm39)	E161G	probably damaging	Het
Tmed10	T	C	12: 85,397,621 (GRCm39)	I123V	probably benign	Het
Ttf1	T	C	2: 28,969,492 (GRCm39)		probably null	Het
Tubg1	A	G	11: 101,016,886 (GRCm39)	D396G	probably damaging	Het
Uhmk1	A	G	1: 170,034,913 (GRCm39)		probably null	Het
Unc13a	C	T	8: 72,103,221 (GRCm39)	A922T	probably benign	Het
Usp24	T	A	4: 106,219,379 (GRCm39)	V525E	probably damaging	Het
Usp28	C	A	9: 48,947,037 (GRCm39)	Q823K	probably damaging	Het
Vldlr	A	T	19: 27,224,031 (GRCm39)	I764F	probably benign	Het
Vmn2r88	T	C	14: 51,648,641 (GRCm39)	Y62H		Het
Zfp423	T	A	8: 88,507,725 (GRCm39)	N873I	possibly damaging	Het

Other mutations in Pcdhga4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
PIT1430001:Pcdhga4	UTSW	18	37,819,267 (GRCm39)	missense	probably benign	0.00
R3828:Pcdhga4	UTSW	18	37,820,654 (GRCm39)	missense	possibly damaging	0.62
R3970:Pcdhga4	UTSW	18	37,820,654 (GRCm39)	missense	possibly damaging	0.62
R4080:Pcdhga4	UTSW	18	37,818,832 (GRCm39)	missense	probably damaging	1.00
R4356:Pcdhga4	UTSW	18	37,820,664 (GRCm39)	missense	probably damaging	1.00
R4834:Pcdhga4	UTSW	18	37,818,490 (GRCm39)	missense	probably benign	0.01
R4983:Pcdhga4	UTSW	18	37,819,572 (GRCm39)	missense	probably damaging	1.00
R5076:Pcdhga4	UTSW	18	37,818,648 (GRCm39)	missense	probably benign	0.43
R5186:Pcdhga4	UTSW	18	37,820,479 (GRCm39)	missense	probably benign	0.07
R5194:Pcdhga4	UTSW	18	37,820,794 (GRCm39)	missense	probably benign	0.08
R5326:Pcdhga4	UTSW	18	37,819,651 (GRCm39)	missense	probably damaging	0.98
R5333:Pcdhga4	UTSW	18	37,818,477 (GRCm39)	missense	probably benign	0.00
R5373:Pcdhga4	UTSW	18	37,818,649 (GRCm39)	missense	probably damaging	1.00
R5374:Pcdhga4	UTSW	18	37,818,649 (GRCm39)	missense	probably damaging	1.00
R5419:Pcdhga4	UTSW	18	37,819,798 (GRCm39)	missense	probably damaging	1.00
R5542:Pcdhga4	UTSW	18	37,819,651 (GRCm39)	missense	probably damaging	0.98
R5878:Pcdhga4	UTSW	18	37,820,739 (GRCm39)	missense	probably benign	0.03
R5996:Pcdhga4	UTSW	18	37,818,991 (GRCm39)	missense	probably benign	0.03
R6056:Pcdhga4	UTSW	18	37,819,383 (GRCm39)	missense	probably benign	0.00
R6083:Pcdhga4	UTSW	18	37,820,478 (GRCm39)	missense	probably damaging	0.98
R6155:Pcdhga4	UTSW	18	37,819,546 (GRCm39)	missense	probably damaging	0.98
R6208:Pcdhga4	UTSW	18	37,819,762 (GRCm39)	missense	probably damaging	1.00
R6306:Pcdhga4	UTSW	18	37,818,966 (GRCm39)	missense	probably damaging	1.00
R6580:Pcdhga4	UTSW	18	37,820,370 (GRCm39)	missense	possibly damaging	0.93
R6936:Pcdhga4	UTSW	18	37,820,458 (GRCm39)	missense	possibly damaging	0.84
R7132:Pcdhga4	UTSW	18	37,820,430 (GRCm39)	missense	probably damaging	1.00
R7159:Pcdhga4	UTSW	18	37,819,972 (GRCm39)	missense	probably damaging	1.00
R7257:Pcdhga4	UTSW	18	37,820,451 (GRCm39)	missense	probably damaging	0.99
R7263:Pcdhga4	UTSW	18	37,819,873 (GRCm39)	missense	probably benign	0.42
R7825:Pcdhga4	UTSW	18	37,820,374 (GRCm39)	missense	probably damaging	1.00
R7882:Pcdhga4	UTSW	18	37,819,681 (GRCm39)	missense	probably damaging	1.00
R7916:Pcdhga4	UTSW	18	37,818,502 (GRCm39)	missense	probably benign	0.22
R8053:Pcdhga4	UTSW	18	37,819,308 (GRCm39)	missense	probably benign	0.07
R9184:Pcdhga4	UTSW	18	37,820,460 (GRCm39)	missense	possibly damaging	0.95
R9292:Pcdhga4	UTSW	18	37,819,713 (GRCm39)	missense	probably benign	0.00
R9417:Pcdhga4	UTSW	18	37,820,560 (GRCm39)	missense	probably damaging	1.00
R9562:Pcdhga4	UTSW	18	37,819,527 (GRCm39)	missense	probably benign	0.03

Predicted Primers

PCR Primer
(F):5'- AGCTCTATCCAGGAAGCTTCTTC -3'
(R):5'- GATAACCTGGGCATTCTCACC -3'

Sequencing Primer
(F):5'- TTCCCCAGGCACAGTGATTG -3'
(R):5'- ACCACTGTCTGGGTCCTG -3'

Posted On

2022-07-18