Mutagenetix > Incidental Mutation

Incidental Mutation 'R1540:Col4a6'

171698

Institutional Source

Beutler Lab

Gene Symbol

Col4a6

Ensembl Gene

ENSMUSG00000031273

Gene Name

collagen, type IV, alpha 6

Synonyms

MMRRC Submission

039579-MU

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R1540 (G1)

Quality Score

222

Status

Validated

Chromosome

Chromosomal Location

139948399-140257072 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 140010854 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Threonine to Alanine at position 129 (T129A)

Ref Sequence

ENSEMBL: ENSMUSP00000098765 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101205]

AlphaFold

B1AVK5

Predicted Effect

probably damaging
Transcript: ENSMUST00000101205
AA Change: T129A

PolyPhen 2 Score 0.999 (Sensitivity: 0.14; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000098765
Gene: ENSMUSG00000031273
AA Change: T129A

Domain	Start	End	E-Value	Type
signal peptide	1	19	N/A	INTRINSIC
Pfam:Collagen	45	106	2e-10	PFAM
Pfam:Collagen	101	162	7.5e-11	PFAM
Pfam:Collagen	165	222	2.1e-10	PFAM
low complexity region	251	277	N/A	INTRINSIC
Pfam:Collagen	282	346	1.8e-11	PFAM
Pfam:Collagen	355	416	1.1e-10	PFAM
low complexity region	421	442	N/A	INTRINSIC
Pfam:Collagen	487	551	4e-11	PFAM
Pfam:Collagen	593	654	1.4e-8	PFAM
low complexity region	660	680	N/A	INTRINSIC
Pfam:Collagen	707	757	5e-9	PFAM
Pfam:Collagen	755	818	1.8e-10	PFAM
low complexity region	867	885	N/A	INTRINSIC
Pfam:Collagen	894	959	1.4e-10	PFAM
low complexity region	990	1002	N/A	INTRINSIC
Pfam:Collagen	1010	1075	5.1e-11	PFAM
Pfam:Collagen	1075	1138	3e-10	PFAM
Pfam:Collagen	1132	1192	2e-11	PFAM
Pfam:Collagen	1193	1252	7e-11	PFAM
Pfam:Collagen	1255	1316	3.1e-10	PFAM
Pfam:Collagen	1310	1370	4.8e-11	PFAM
Pfam:Collagen	1375	1433	2.3e-10	PFAM
C4	1467	1574	3.11e-62	SMART
C4	1575	1690	8.66e-70	SMART

Meta Mutation Damage Score

0.0855

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 93.0%

Validation Efficiency

96% (72/75)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes one of the six subunits of type IV collagen, the major structural component of basement membranes. Like the other members of the type IV collagen gene family, this gene is organized in a head-to-head conformation with another type IV collagen gene, alpha 5 type IV collagen, so that the gene pair shares a common promoter. Deletions in the alpha 5 gene that extend into the alpha 6 gene result in diffuse leiomyomatosis accompanying the X-linked Alport syndrome caused by the deletion in the alpha 5 gene. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2013]
PHENOTYPE: Male mice hemizygous for a knock-out allele are viable, fertile and healthy with no apparent defects in the topology of neuromuscular junctions in the diaphragm muscle. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 72 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Agl	A	G	3: 116,574,384 (GRCm39)	C767R	probably benign	Het
Anpep	C	T	7: 79,488,004 (GRCm39)	E518K	probably benign	Het
Ap3d1	A	T	10: 80,551,775 (GRCm39)	I644N	probably benign	Het
Asb16	A	G	11: 102,163,402 (GRCm39)	I131V	probably benign	Het
Atp6v0a2	C	A	5: 124,784,638 (GRCm39)	A307D	probably damaging	Het
C1qtnf1	C	T	11: 118,338,749 (GRCm39)	H140Y	probably benign	Het
Cacna1g	T	A	11: 94,347,865 (GRCm39)	D741V	probably damaging	Het
Caprin2	T	A	6: 148,777,969 (GRCm39)	T211S	probably benign	Het
Carmil1	T	C	13: 24,283,037 (GRCm39)	E89G	possibly damaging	Het
Casz1	T	A	4: 149,027,357 (GRCm39)		probably benign	Het
Catsperb	G	A	12: 101,378,589 (GRCm39)	R30Q	probably benign	Het
Ccdc102a	A	T	8: 95,634,341 (GRCm39)		probably null	Het
Ccdc110	G	T	8: 46,395,362 (GRCm39)	E418*	probably null	Het
Ccdc90b	C	T	7: 92,231,024 (GRCm39)	A210V	probably benign	Het
Cdadc1	G	T	14: 59,823,532 (GRCm39)	A320E	probably damaging	Het
Cdadc1	T	A	14: 59,823,541 (GRCm39)	Q317L	probably damaging	Het
Cep170	C	A	1: 176,567,498 (GRCm39)	W1396L	probably damaging	Het
Ctcfl	C	T	2: 172,954,141 (GRCm39)	D319N	probably benign	Het
Dclk1	T	C	3: 55,385,244 (GRCm39)	S45P	probably damaging	Het
Efcab3	T	C	11: 104,999,726 (GRCm39)	I5581T	probably benign	Het
Evi2	T	C	11: 79,406,412 (GRCm39)	I388V	probably benign	Het
Fbxl5	A	T	5: 43,915,978 (GRCm39)	V435E	possibly damaging	Het
Fig4	A	T	10: 41,064,582 (GRCm39)	M887K	possibly damaging	Het
Glt8d1	G	A	14: 30,733,549 (GRCm39)	V345I	probably benign	Het
Gm5709	T	C	3: 59,526,073 (GRCm39)		noncoding transcript	Het
Hsp90b1	A	G	10: 86,529,906 (GRCm39)	F264L	probably damaging	Het
Id3	A	G	4: 135,871,250 (GRCm39)	S21G	possibly damaging	Het
Ighe	T	A	12: 113,235,066 (GRCm39)	N365Y	unknown	Het
Il17rd	T	G	14: 26,821,915 (GRCm39)	M403R	probably damaging	Het
Ints10	A	G	8: 69,249,365 (GRCm39)		probably benign	Het
Kcnc4	T	A	3: 107,352,743 (GRCm39)		probably null	Het
Kctd19	A	G	8: 106,114,511 (GRCm39)	S517P	probably damaging	Het
Lama5	A	G	2: 179,821,944 (GRCm39)	F2964L	probably benign	Het
Lin54	A	T	5: 100,628,109 (GRCm39)	N31K	probably damaging	Het
Lrrc8e	A	G	8: 4,284,990 (GRCm39)	K405R	probably benign	Het
Lyst	T	A	13: 13,809,686 (GRCm39)	M452K	possibly damaging	Het
Mroh7	A	G	4: 106,560,273 (GRCm39)	L677P	probably benign	Het
Mrps27	T	A	13: 99,541,558 (GRCm39)	F221I	probably benign	Het
Nhlrc1	C	T	13: 47,167,820 (GRCm39)	V146M	probably damaging	Het
Nlrp9b	T	A	7: 19,782,772 (GRCm39)	C895*	probably null	Het
Nod1	T	C	6: 54,920,960 (GRCm39)	T453A	probably benign	Het
Nodal	T	C	10: 61,258,764 (GRCm39)	V67A	probably damaging	Het
Ntsr1	T	C	2: 180,184,440 (GRCm39)	L381P	probably damaging	Het
Or13c25	T	C	4: 52,910,996 (GRCm39)	D266G	probably benign	Het
Or2b2b	T	A	13: 21,858,700 (GRCm39)	Q138L	probably benign	Het
Or9e1	T	A	11: 58,732,477 (GRCm39)	M179K	probably benign	Het
P2ry14	T	A	3: 59,022,686 (GRCm39)	K267M	probably benign	Het
Pcdh1	T	C	18: 38,322,779 (GRCm39)	N1018S	probably benign	Het
Pkn3	G	A	2: 29,974,703 (GRCm39)	V406I	probably damaging	Het
Prkcb	C	T	7: 122,226,916 (GRCm39)	T634I	probably damaging	Het
Psme2b	T	A	11: 48,836,209 (GRCm39)		probably null	Het
Ptgfrn	A	G	3: 100,967,970 (GRCm39)	I541T	probably benign	Het
Ptpro	T	A	6: 137,420,592 (GRCm39)	V1007D	probably damaging	Het
Ralgapb	T	C	2: 158,307,746 (GRCm39)	V684A	probably benign	Het
Rbbp5	C	T	1: 132,422,020 (GRCm39)	R307*	probably null	Het
Rcor1	T	A	12: 111,070,037 (GRCm39)		probably benign	Het
Rlbp1	C	T	7: 79,029,808 (GRCm39)	A142T	probably damaging	Het
Rps6ka2	A	G	17: 7,560,305 (GRCm39)	E581G	probably null	Het
Sars1	A	T	3: 108,340,461 (GRCm39)	V155E	probably benign	Het
Sec31a	G	C	5: 100,523,178 (GRCm39)	P569A	probably damaging	Het
Selenof	A	T	3: 144,300,685 (GRCm39)	K111*	probably null	Het
Serpinb7	C	T	1: 107,355,998 (GRCm39)	A7V	possibly damaging	Het
Smc4	T	A	3: 68,924,105 (GRCm39)	Y298N	probably damaging	Het
Snrpa1	T	A	7: 65,720,409 (GRCm39)	I204N	probably damaging	Het
Spry4	T	G	18: 38,734,740 (GRCm39)		probably benign	Het
Tcea2	A	G	2: 181,328,751 (GRCm39)	N261S	possibly damaging	Het
Tmem59l	A	G	8: 70,937,804 (GRCm39)	F192S	probably benign	Het
Tnr	T	A	1: 159,677,675 (GRCm39)	I20N	probably damaging	Het
Ttll5	C	T	12: 85,938,982 (GRCm39)	Q427*	probably null	Het
Vps45	C	T	3: 95,955,658 (GRCm39)	A111T	probably damaging	Het
Zfp395	T	C	14: 65,630,523 (GRCm39)	S358P	probably benign	Het
Zfp438	A	G	18: 5,210,740 (GRCm39)	V766A	probably benign	Het

Other mutations in Col4a6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0606:Col4a6	UTSW	X	139,975,219 (GRCm39)	splice site	probably benign
R3772:Col4a6	UTSW	X	139,955,196 (GRCm39)	missense	probably damaging	1.00
R8673:Col4a6	UTSW	X	140,017,173 (GRCm39)	missense	probably damaging	1.00

Predicted Primers

PCR Primer
(F):5'- TCTTGCATTGGGCAAGGTAGTACAG -3'
(R):5'- TCCGTTCAGAAAGCCATCCAGC -3'

Sequencing Primer
(F):5'- TAGTACAGTGGCTGTCTACAAG -3'
(R):5'- GTCTGGTCTGAGGAATCTCAAACC -3'

Posted On

2014-04-13