Mutagenetix > Incidental Mutation

Incidental Mutation 'R5447:Hoxd4'

429107

Institutional Source

Beutler Lab

Gene Symbol

Hoxd4

Ensembl Gene

ENSMUSG00000101174

Gene Name

homeobox D4

Synonyms

Hox-5.1, Hox-4.2

MMRRC Submission

043012-MU

Accession Numbers

Essential gene?

Possibly non essential (E-score: 0.495) question?

Stock #

R5447 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

74552322-74559504 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 74557687 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 22 (E22G)

Ref Sequence

ENSEMBL: ENSMUSP00000051355 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047904] [ENSMUST00000053932] [ENSMUST00000111980] [ENSMUST00000111983]

AlphaFold

P10628

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047904
AA Change: E22G

PolyPhen 2 Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000047949
Gene: ENSMUSG00000115956
AA Change: E22G

Domain	Start	End	E-Value	Type
low complexity region	63	70	N/A	INTRINSIC
low complexity region	91	110	N/A	INTRINSIC
low complexity region	112	123	N/A	INTRINSIC
HOX	152	214	2.46e-26	SMART
low complexity region	220	229	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000053932
AA Change: E22G

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)

SMART Domains

Protein: ENSMUSP00000051355
Gene: ENSMUSG00000100642
AA Change: E22G

Domain	Start	End	E-Value	Type
low complexity region	93	135	N/A	INTRINSIC
low complexity region	141	159	N/A	INTRINSIC
HOX	195	257	5.83e-28	SMART
Pfam:DUF4074	370	431	1.4e-33	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000083566

Predicted Effect

possibly damaging
Transcript: ENSMUST00000111980
AA Change: E22G

PolyPhen 2 Score 0.719 (Sensitivity: 0.86; Specificity: 0.92)

SMART Domains

Protein: ENSMUSP00000107611
Gene: ENSMUSG00000101174
AA Change: E22G

Domain	Start	End	E-Value	Type
low complexity region	63	70	N/A	INTRINSIC
low complexity region	91	110	N/A	INTRINSIC
low complexity region	112	123	N/A	INTRINSIC
HOX	152	214	2.46e-26	SMART
low complexity region	220	229	N/A	INTRINSIC

Predicted Effect

probably benign
Transcript: ENSMUST00000111983

SMART Domains

Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277

Domain	Start	End	E-Value	Type
low complexity region	93	135	N/A	INTRINSIC
low complexity region	141	159	N/A	INTRINSIC
HOX	195	257	5.83e-28	SMART
Pfam:DUF4074	369	431	8.9e-35	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000144040

Meta Mutation Damage Score

0.2461

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.2%
20x: 95.1%

Validation Efficiency

97% (71/73)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5' end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in determining positional values in developing limb buds. Alternatively spliced variants have been described but their full length nature has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Both homozygotes and heterozygotes for a targeted null mutation exhibit homeotic transformations of the second cervical vertebrae and malformed neural arches of C1 to C3 and of the basioccipital bone. Mutants show variable penetrance and expressivity. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abcb5	T	C	12: 118,891,061 (GRCm39)	I479V	probably damaging	Het
Adam30	A	G	3: 98,068,659 (GRCm39)	D164G	probably benign	Het
Adgrl3	T	A	5: 81,613,188 (GRCm39)		probably benign	Het
Adrb1	T	C	19: 56,711,519 (GRCm39)	I239T	probably benign	Het
Albfm1	C	A	5: 90,732,169 (GRCm39)	A458E	probably damaging	Het
B4galnt3	T	C	6: 120,192,018 (GRCm39)	T572A	probably benign	Het
Baz2b	T	C	2: 59,744,332 (GRCm39)	E1391G	probably damaging	Het
BC016579	A	G	16: 45,469,252 (GRCm39)	V72A	probably benign	Het
Btnl10	A	T	11: 58,813,144 (GRCm39)	I258F	probably benign	Het
Cdh5	A	T	8: 104,855,994 (GRCm39)	D309V	probably damaging	Het
Cdhr2	A	G	13: 54,881,063 (GRCm39)	D1042G	probably damaging	Het
Clk2	G	T	3: 89,074,498 (GRCm39)	V53F	possibly damaging	Het
Cyfip2	T	C	11: 46,182,413 (GRCm39)	D15G	possibly damaging	Het
Dip2b	C	T	15: 100,109,867 (GRCm39)	R1451C	probably damaging	Het
Dmbt1	A	G	7: 130,721,240 (GRCm39)	Y1836C	probably damaging	Het
Dysf	T	C	6: 84,172,245 (GRCm39)	F1905L	probably damaging	Het
E130114P18Rik	A	G	4: 97,578,955 (GRCm39)	S7P	unknown	Het
Fam110a	T	C	2: 151,812,629 (GRCm39)	E47G	probably damaging	Het
Gemin6	T	G	17: 80,535,178 (GRCm39)	V46G	probably damaging	Het
Helb	T	A	10: 119,938,806 (GRCm39)	D556V	possibly damaging	Het
Hsd17b8	A	T	17: 34,245,886 (GRCm39)	V202D	probably damaging	Het
Il1rl2	T	G	1: 40,368,316 (GRCm39)	I162R	probably damaging	Het
Lhfpl5	A	G	17: 28,795,071 (GRCm39)	T33A	probably damaging	Het
Mapk8ip3	G	A	17: 25,118,163 (GRCm39)	A1283V	probably benign	Het
Mettl13	A	G	1: 162,363,449 (GRCm39)	V227A	probably benign	Het
Mmgt2	T	A	11: 62,555,824 (GRCm39)	C57*	probably null	Het
Muc4	G	C	16: 32,753,919 (GRCm38)	R1265P	probably benign	Het
Mylk2	T	C	2: 152,754,430 (GRCm39)	S175P	probably damaging	Het
Neu4	C	T	1: 93,950,140 (GRCm39)	T33M	probably damaging	Het
Nfs1	C	T	2: 155,984,056 (GRCm39)	R107H	probably benign	Het
Nfxl1	C	T	5: 72,686,512 (GRCm39)	R563Q	probably benign	Het
Nid1	A	G	13: 13,612,495 (GRCm39)	D70G	probably benign	Het
Nup160	C	A	2: 90,555,959 (GRCm39)	Q1220K	possibly damaging	Het
Or1ad8	G	A	11: 50,898,170 (GRCm39)	V124M	possibly damaging	Het
Or1e22	A	G	11: 73,377,002 (GRCm39)	V216A	probably benign	Het
Or52s6	A	C	7: 103,092,147 (GRCm39)	M61R	probably damaging	Het
Or5k8	A	T	16: 58,644,846 (GRCm39)	C75*	probably null	Het
Pdgfrb	T	A	18: 61,201,180 (GRCm39)	V422E	probably damaging	Het
Pear1	G	A	3: 87,666,449 (GRCm39)	R85C	probably damaging	Het
Pkhd1	T	A	1: 20,309,609 (GRCm39)	M2780L	probably benign	Het
Ppp4r4	T	C	12: 103,550,410 (GRCm39)	V62A	possibly damaging	Het
Prol1	C	T	5: 88,476,125 (GRCm39)	P172S	unknown	Het
Proz	A	G	8: 13,122,578 (GRCm39)	I231V	probably benign	Het
Ptch1	T	G	13: 63,675,059 (GRCm39)	M718L	probably benign	Het
Ptprs	A	G	17: 56,736,128 (GRCm39)	C102R	possibly damaging	Het
Robo2	A	T	16: 73,770,654 (GRCm39)	Y490*	probably null	Het
Rptor	G	A	11: 119,734,539 (GRCm39)	G514D	probably damaging	Het
Scara5	CG	C	14: 65,997,111 (GRCm39)		probably null	Het
Skint6	T	A	4: 112,963,106 (GRCm39)	S442C	probably benign	Het
Snw1	T	C	12: 87,502,485 (GRCm39)	E303G	probably benign	Het
Sp110	C	G	1: 85,516,839 (GRCm39)	E219D	probably damaging	Het
Stam2	G	A	2: 52,626,305 (GRCm39)		probably benign	Het
Stk10	C	T	11: 32,554,166 (GRCm39)	Q618*	probably null	Het
Tmc3	A	T	7: 83,271,569 (GRCm39)	E907V	possibly damaging	Het
Ttn	A	T	2: 76,641,587 (GRCm39)	L5176Q	possibly damaging	Het
Ttn	T	A	2: 76,729,451 (GRCm39)		probably benign	Het
Vps39	T	C	2: 120,183,413 (GRCm39)	D19G	probably benign	Het
Zan	T	C	5: 137,470,453 (GRCm39)	S229G	probably damaging	Het
Zfp141	A	T	7: 42,124,983 (GRCm39)	C496*	probably null	Het
Zgrf1	T	C	3: 127,356,768 (GRCm39)	S665P	possibly damaging	Het

Other mutations in Hoxd4

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02034:Hoxd4	APN	2	74,558,750 (GRCm39)	missense	probably damaging	0.98
IGL03403:Hoxd4	APN	2	74,558,681 (GRCm39)	missense	possibly damaging	0.93
R0153:Hoxd4	UTSW	2	74,557,801 (GRCm39)	missense	probably damaging	0.96
R3424:Hoxd4	UTSW	2	74,557,657 (GRCm39)	missense	probably damaging	1.00
R5715:Hoxd4	UTSW	2	74,557,708 (GRCm39)	missense	probably damaging	1.00
R6197:Hoxd4	UTSW	2	74,558,807 (GRCm39)	missense	possibly damaging	0.85
R6264:Hoxd4	UTSW	2	74,557,729 (GRCm39)	missense	possibly damaging	0.53
R6310:Hoxd4	UTSW	2	74,558,734 (GRCm39)	missense	possibly damaging	0.84
R6336:Hoxd4	UTSW	2	74,557,705 (GRCm39)	missense	probably damaging	1.00
R6921:Hoxd4	UTSW	2	74,558,836 (GRCm39)	missense	possibly damaging	0.73
R9246:Hoxd4	UTSW	2	74,558,747 (GRCm39)	missense	possibly damaging	0.86

Predicted Primers

PCR Primer
(F):5'- ATGGCCGCCCAACTTTATTC -3'
(R):5'- TCATCCAAGGGTAGACCACAGC -3'

Sequencing Primer
(F):5'- TTATTCAGTTGACAGCAAGTAGGAG -3'
(R):5'- ACCGTAATGACTTCCCGGG -3'

Posted On

2016-09-06