Mutagenetix > Incidental Mutation

Incidental Mutation 'R6115:Alx1'

485090

Institutional Source

Beutler Lab

Gene Symbol

Alx1

Ensembl Gene

ENSMUSG00000036602

Gene Name

ALX homeobox 1

Synonyms

Cart1

MMRRC Submission

044264-MU

Accession Numbers

Essential gene?

Essential (E-score: 1.000) question?

Stock #

R6115 (G1)

Quality Score

168.009

Status

Validated

Chromosome

Chromosomal Location

102843708-102865501 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 102864304 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Proline to Leucine at position 55 (P55L)

Ref Sequence

ENSEMBL: ENSMUSP00000152017 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000040859] [ENSMUST00000167156] [ENSMUST00000217946] [ENSMUST00000218282] [ENSMUST00000218681] [ENSMUST00000219194]

AlphaFold

Q8C8B0

Predicted Effect

probably benign
Transcript: ENSMUST00000040859
AA Change: P55L

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000042512
Gene: ENSMUSG00000036602
AA Change: P55L

Domain	Start	End	E-Value	Type
HOX	132	194	1.84e-25	SMART
Pfam:OAR	301	321	7.3e-13	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000167156
AA Change: P55L

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

SMART Domains

Protein: ENSMUSP00000129230
Gene: ENSMUSG00000036602
AA Change: P55L

Domain	Start	End	E-Value	Type
HOX	132	194	1.84e-25	SMART
Pfam:OAR	302	320	2.3e-12	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000170026

Predicted Effect

possibly damaging
Transcript: ENSMUST00000217946
AA Change: P55L

PolyPhen 2 Score 0.780 (Sensitivity: 0.85; Specificity: 0.93)

Predicted Effect

probably benign
Transcript: ENSMUST00000218282
AA Change: P55L

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000218508

Predicted Effect

possibly damaging
Transcript: ENSMUST00000218681
AA Change: P55L

PolyPhen 2 Score 0.625 (Sensitivity: 0.87; Specificity: 0.91)

Predicted Effect

probably benign
Transcript: ENSMUST00000219194
AA Change: P55L

PolyPhen 2 Score 0.109 (Sensitivity: 0.93; Specificity: 0.86)

Meta Mutation Damage Score

0.0698

Coding Region Coverage

1x: 99.9%
3x: 99.7%
10x: 98.5%
20x: 95.9%

Validation Efficiency

98% (51/52)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The specific function of this gene has yet to be determined in humans; however, in rodents, it is necessary for survival of the forebrain mesenchyme and may also be involved in development of the cervix. Mutations in the mouse gene lead to neural tube defects such as acrania and meroanencephaly. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous mutant mice exhibit perinatal lethality with acrania and meroanencephaly, but the neural tube closure defect can be ameliorated with prenatal folic acid treatment. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 50 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
0610040J01Rik	C	G	5: 64,055,317 (GRCm39)	Q18E	probably damaging	Het
Acsf3	T	A	8: 123,517,411 (GRCm39)	H402Q	probably damaging	Het
Adam34	T	G	8: 44,105,098 (GRCm39)	Q182H	probably benign	Het
Arhgef38	A	T	3: 132,838,374 (GRCm39)		probably null	Het
Ccdc102a	T	C	8: 95,629,999 (GRCm39)	N514S	probably benign	Het
Corin	T	A	5: 72,518,072 (GRCm39)	T317S	probably damaging	Het
Ctnna2	A	G	6: 77,613,822 (GRCm39)	V256A	probably benign	Het
Dhx29	A	T	13: 113,089,335 (GRCm39)		probably null	Het
Dnah2	C	A	11: 69,337,475 (GRCm39)	D3209Y	probably damaging	Het
Dnhd1	A	G	7: 105,363,194 (GRCm39)	T3919A	probably benign	Het
F7	T	A	8: 13,083,958 (GRCm39)	N214K	probably benign	Het
Fam3b	T	G	16: 97,276,568 (GRCm39)	Q177H	possibly damaging	Het
Fign	T	C	2: 63,809,654 (GRCm39)	I539V	probably benign	Het
Hc	T	G	2: 34,903,050 (GRCm39)	D1067A	probably damaging	Het
Herc6	A	G	6: 57,560,191 (GRCm39)	D77G	probably benign	Het
Hmg20a	A	T	9: 56,397,116 (GRCm39)	E305D	possibly damaging	Het
Il16	G	A	7: 83,301,775 (GRCm39)	Q116*	probably null	Het
Kif13a	T	A	13: 46,954,789 (GRCm39)	I648F	probably damaging	Het
Lactb	G	T	9: 66,874,969 (GRCm39)	N374K	possibly damaging	Het
Lmx1b	T	C	2: 33,459,118 (GRCm39)	D145G	probably damaging	Het
Lrfn4	T	C	19: 4,663,937 (GRCm39)	D199G	probably damaging	Het
Lrrc49	A	T	9: 60,522,444 (GRCm39)	V307E	possibly damaging	Het
Magi1	A	C	6: 93,685,051 (GRCm39)	S776A	possibly damaging	Het
Mthfsl	T	A	9: 88,570,807 (GRCm39)	*147L	probably null	Het
Nsmce4a	G	T	7: 130,148,722 (GRCm39)	Q95K	probably benign	Het
Or1j15	A	T	2: 36,458,963 (GRCm39)	M118L	probably damaging	Het
Or4k37	A	G	2: 111,159,558 (GRCm39)	T265A	probably benign	Het
Or4k49	A	T	2: 111,494,987 (GRCm39)	K139*	probably null	Het
Or5b24	T	C	19: 12,912,948 (GRCm39)	V282A	possibly damaging	Het
Pcdha7	A	G	18: 37,107,788 (GRCm39)	E271G	probably damaging	Het
Pcdhga8	T	A	18: 37,860,596 (GRCm39)	F551I	possibly damaging	Het
Prpf31	T	C	7: 3,642,705 (GRCm39)		probably null	Het
Qrfpr	C	T	3: 36,236,742 (GRCm39)	V220I	possibly damaging	Het
Rnf170	T	C	8: 26,615,994 (GRCm39)	F95S	possibly damaging	Het
Scn9a	T	A	2: 66,393,973 (GRCm39)	Y200F	possibly damaging	Het
Sfpq	A	T	4: 126,915,141 (GRCm39)		probably null	Het
Slc9c1	A	T	16: 45,376,132 (GRCm39)	Y406F	probably damaging	Het
Stk32c	G	T	7: 138,700,628 (GRCm39)	Y200*	probably null	Het
Svil	A	G	18: 5,108,675 (GRCm39)	R1938G	probably damaging	Het
Sycp2	G	C	2: 177,990,038 (GRCm39)	R1403G	probably benign	Het
Tm9sf4	T	C	2: 153,024,409 (GRCm39)		probably null	Het
Tmc3	A	T	7: 83,264,170 (GRCm39)	M633L	possibly damaging	Het
Tmem163	T	C	1: 127,605,185 (GRCm39)	D61G	possibly damaging	Het
Unc5b	C	A	10: 60,613,325 (GRCm39)	A304S	probably benign	Het
Vmn2r106	G	A	17: 20,488,638 (GRCm39)	P587L	probably benign	Het
Vmn2r18	A	T	5: 151,508,462 (GRCm39)	S221T	possibly damaging	Het
Vmn2r85	T	G	10: 130,258,672 (GRCm39)	Y461S	probably damaging	Het
Yod1	T	C	1: 130,646,800 (GRCm39)	F226L	possibly damaging	Het
Zbtb4	T	C	11: 69,667,148 (GRCm39)	I151T	probably damaging	Het
Zfp110	A	T	7: 12,583,701 (GRCm39)	Q783L	probably damaging	Het

Other mutations in Alx1

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02331:Alx1	APN	10	102,858,160 (GRCm39)	missense	possibly damaging	0.93
IGL02508:Alx1	APN	10	102,858,054 (GRCm39)	missense	probably damaging	0.99
IGL03079:Alx1	APN	10	102,845,209 (GRCm39)	missense	probably damaging	1.00
R1345:Alx1	UTSW	10	102,864,353 (GRCm39)	missense	possibly damaging	0.86
R1370:Alx1	UTSW	10	102,864,353 (GRCm39)	missense	possibly damaging	0.86
R1846:Alx1	UTSW	10	102,861,165 (GRCm39)	missense	possibly damaging	0.88
R1912:Alx1	UTSW	10	102,861,222 (GRCm39)	missense	probably damaging	1.00
R4649:Alx1	UTSW	10	102,845,193 (GRCm39)	missense	probably damaging	0.99
R4767:Alx1	UTSW	10	102,861,047 (GRCm39)	nonsense	probably null
R5484:Alx1	UTSW	10	102,861,177 (GRCm39)	missense	probably damaging	0.99
R5979:Alx1	UTSW	10	102,858,120 (GRCm39)	missense	probably damaging	1.00
R6919:Alx1	UTSW	10	102,861,061 (GRCm39)	missense	probably damaging	1.00
R7781:Alx1	UTSW	10	102,845,053 (GRCm39)	missense	probably damaging	0.99
R8166:Alx1	UTSW	10	102,845,224 (GRCm39)	missense	probably damaging	1.00
R8238:Alx1	UTSW	10	102,858,076 (GRCm39)	missense	possibly damaging	0.80
R8275:Alx1	UTSW	10	102,864,250 (GRCm39)	missense	probably benign	0.04
R9219:Alx1	UTSW	10	102,858,121 (GRCm39)	missense	probably damaging	0.98
R9323:Alx1	UTSW	10	102,858,124 (GRCm39)	nonsense	probably null
R9482:Alx1	UTSW	10	102,864,335 (GRCm39)	missense	probably benign
R9654:Alx1	UTSW	10	102,858,093 (GRCm39)	missense	probably benign	0.02

Predicted Primers

PCR Primer
(F):5'- CAGCAATCTGGATTCCTCTTGC -3'
(R):5'- CCAGGATTATGGAGTTTCTGAGC -3'

Sequencing Primer
(F):5'- TACCTCACTTCGGGGAAGGATG -3'
(R):5'- TCTGAGCGAGAAGTTTGCCC -3'

Posted On

2017-08-16