Mutagenetix > Incidental Mutation

Incidental Mutation 'R3983:Hoxa4'

350680

Institutional Source

Beutler Lab

Gene Symbol

Hoxa4

Ensembl Gene

ENSMUSG00000000942

Gene Name

homeobox A4

Synonyms

Hox-1.4

MMRRC Submission

040944-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.490) question?

Stock #

R3983 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

52166662-52168683 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 52167657 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Asparagine at position 175 (Y175N)

Ref Sequence

ENSEMBL: ENSMUSP00000098943 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000101395] [ENSMUST00000114434] [ENSMUST00000128102]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000101395
AA Change: Y175N

PolyPhen 2 Score 0.188 (Sensitivity: 0.92; Specificity: 0.87)

SMART Domains

Protein: ENSMUSP00000098943
Gene: ENSMUSG00000000942
AA Change: Y175N

Domain	Start	End	E-Value	Type
low complexity region	14	23	N/A	INTRINSIC
low complexity region	25	45	N/A	INTRINSIC
low complexity region	48	95	N/A	INTRINSIC
low complexity region	101	126	N/A	INTRINSIC
HOX	180	242	1.52e-26	SMART
low complexity region	265	275	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000114434

SMART Domains

Protein: ENSMUSP00000110077
Gene: ENSMUSG00000079560

Domain	Start	End	E-Value	Type
low complexity region	76	131	N/A	INTRINSIC
HOX	192	254	3.35e-28	SMART
low complexity region	287	302	N/A	INTRINSIC
low complexity region	304	326	N/A	INTRINSIC
Pfam:DUF4074	377	441	9e-32	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000128102

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136806

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000139055

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191326

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000191453

Meta Mutation Damage Score

0.4421

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.5%

Validation Efficiency

100% (65/65)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. [provided by RefSeq, Jul 2008]
PHENOTYPE: Homozygous inactivation of this gene leads to homeotic transformation of cervical vertebrae. Mice homozygous for a knock-out allele also exhibit a hunched appearance of the pectoral girdle. Mice homozygous for a different knock-out allele show additionalsternal defects. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 59 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700093K21Rik	T	A	11: 23,467,220 (GRCm39)	N138Y	possibly damaging	Het
4921504E06Rik	A	G	2: 19,547,180 (GRCm39)		probably null	Het
Abcc6	T	C	7: 45,644,713 (GRCm39)	I821V	probably benign	Het
Adam34	G	A	8: 44,103,806 (GRCm39)	T613I	probably benign	Het
Ap2b1	C	T	11: 83,281,542 (GRCm39)	T816M	probably damaging	Het
Cct2	G	A	10: 116,890,040 (GRCm39)	P10L	probably damaging	Het
Cdc23	C	A	18: 34,770,539 (GRCm39)		probably benign	Het
Chrna2	G	T	14: 66,386,906 (GRCm39)	V351L	probably benign	Het
Clca3a1	T	A	3: 144,461,070 (GRCm39)	T194S	probably benign	Het
Col18a1	C	A	10: 76,924,721 (GRCm39)	D23Y	probably damaging	Het
Cyp2c50	A	C	19: 40,101,962 (GRCm39)	K400T	possibly damaging	Het
Cyp2c54	G	T	19: 40,034,699 (GRCm39)	Q324K	possibly damaging	Het
Dcpp2	T	A	17: 24,119,547 (GRCm39)	Y120*	probably null	Het
Ddx11	C	T	17: 66,441,125 (GRCm39)	R242W	probably damaging	Het
Dnah7b	T	A	1: 46,272,871 (GRCm39)	V2333E	possibly damaging	Het
Duxf4	T	A	10: 58,071,623 (GRCm39)	N197I	possibly damaging	Het
Eno3	T	A	11: 70,552,237 (GRCm39)	F296L	probably damaging	Het
Flnc	G	A	6: 29,442,940 (GRCm39)	V492M	probably damaging	Het
Gdap1	T	G	1: 17,230,131 (GRCm39)		probably benign	Het
Gm1587	C	T	14: 78,032,283 (GRCm39)	E118K	unknown	Het
Gprin3	T	C	6: 59,331,545 (GRCm39)	E254G	possibly damaging	Het
Hcrt	G	A	11: 100,652,679 (GRCm39)	R112C	probably damaging	Het
Hydin	G	A	8: 111,118,957 (GRCm39)	G504R	probably damaging	Het
Il1rl1	A	G	1: 40,485,823 (GRCm39)	R325G	possibly damaging	Het
Kcp	A	T	6: 29,484,636 (GRCm39)	L1314Q	probably damaging	Het
Kdm5b	C	T	1: 134,559,042 (GRCm39)	P1522L	possibly damaging	Het
Kmt2d	T	G	15: 98,743,927 (GRCm39)		probably benign	Het
Map3k20	C	T	2: 72,268,571 (GRCm39)	T526I	probably damaging	Het
Mfap2	A	G	4: 140,741,554 (GRCm39)	Q71R	possibly damaging	Het
Mme	T	A	3: 63,235,485 (GRCm39)	Y178N	probably damaging	Het
Msr1	A	G	8: 40,073,059 (GRCm39)	V164A	possibly damaging	Het
Mybbp1a	T	C	11: 72,337,996 (GRCm39)	V646A	probably damaging	Het
Mybpc3	A	T	2: 90,965,714 (GRCm39)	K1175N	probably benign	Het
Myo1c	T	A	11: 75,552,325 (GRCm39)	L366Q	probably benign	Het
Or12d15	T	C	17: 37,694,289 (GRCm39)	V277A	possibly damaging	Het
Or1e22	A	G	11: 73,376,961 (GRCm39)	S230P	possibly damaging	Het
Or6f1	A	G	7: 85,970,942 (GRCm39)	Y73H	probably damaging	Het
Palmd	T	C	3: 116,717,472 (GRCm39)	T342A	probably benign	Het
Pde4d	A	G	13: 109,876,940 (GRCm39)	T29A	probably benign	Het
Rapgef5	A	G	12: 117,692,405 (GRCm39)	E563G	possibly damaging	Het
Rdh19	A	G	10: 127,686,017 (GRCm39)	N43S	probably benign	Het
Rnf44	A	C	13: 54,830,961 (GRCm39)	S98R	probably damaging	Het
Samhd1	C	A	2: 156,965,369 (GRCm39)	V149L	possibly damaging	Het
Scn4a	G	T	11: 106,238,644 (GRCm39)	N214K	probably damaging	Het
Sh3bp4	A	G	1: 89,073,591 (GRCm39)	N813S	probably benign	Het
Sirt3	A	T	7: 140,458,025 (GRCm39)	C41*	probably null	Het
Speg	C	A	1: 75,399,191 (GRCm39)	P2213T	probably benign	Het
Srcin1	T	G	11: 97,416,379 (GRCm39)	E951A	probably damaging	Het
Syn2	C	G	6: 115,214,259 (GRCm39)	T161S	probably benign	Het
Tbc1d4	T	C	14: 101,744,649 (GRCm39)	T326A	probably benign	Het
Tcstv2a	G	T	13: 120,725,815 (GRCm39)	A160S	possibly damaging	Het
Tes	T	A	6: 17,099,700 (GRCm39)		probably null	Het
Thoc2l	T	C	5: 104,668,889 (GRCm39)	V1137A	probably benign	Het
Tln1	T	C	4: 43,553,030 (GRCm39)	T354A	probably damaging	Het
Ttn	G	T	2: 76,632,705 (GRCm39)	S12370R	possibly damaging	Het
Twsg1	T	C	17: 66,236,758 (GRCm39)	T91A	probably benign	Het
Vmn1r181	C	T	7: 23,684,234 (GRCm39)	T233I	probably benign	Het
Wee2	A	T	6: 40,432,175 (GRCm39)	N248I	possibly damaging	Het
Zfp740	G	T	15: 102,116,678 (GRCm39)	C56F	probably benign	Het

Other mutations in Hoxa4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01399:Hoxa4	APN	6	52,167,393 (GRCm39)	missense	probably damaging	0.98
BB009:Hoxa4	UTSW	6	52,167,397 (GRCm39)	missense	probably damaging	1.00
BB019:Hoxa4	UTSW	6	52,167,397 (GRCm39)	missense	probably damaging	1.00
PIT1430001:Hoxa4	UTSW	6	52,168,199 (GRCm39)	missense	possibly damaging	0.47
R7087:Hoxa4	UTSW	6	52,168,271 (GRCm39)	missense	probably damaging	0.99
R7592:Hoxa4	UTSW	6	52,168,520 (GRCm39)	missense	unknown
R7932:Hoxa4	UTSW	6	52,167,397 (GRCm39)	missense	probably damaging	1.00
R7971:Hoxa4	UTSW	6	52,168,711 (GRCm39)	intron	probably benign
R8134:Hoxa4	UTSW	6	52,167,537 (GRCm39)	missense	possibly damaging	0.66
Z1177:Hoxa4	UTSW	6	52,168,616 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- GCAGTGTTGGAAGATCGCATC -3'
(R):5'- TCCCGTTGTCAATAGCCTGTG -3'

Sequencing Primer
(F):5'- CACTTCATTCTCCGGTTCTGAAAC -3'
(R):5'- AGCCTGTGAAACATTTTCTTTGC -3'

Posted On

2015-10-08