Mutagenetix > Incidental Mutation

Incidental Mutation 'R5256:Hoxd3'

399577

Institutional Source

Beutler Lab

Gene Symbol

Hoxd3

Ensembl Gene

ENSMUSG00000079277

Gene Name

homeobox D3

Synonyms

Hox-5.5, Hox-4.1

MMRRC Submission

042827-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.858) question?

Stock #

R5256 (G1)

Quality Score

216

Status

Validated

Chromosome

Chromosomal Location

74542337-74578615 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 74577211 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Valine to Isoleucine at position 364 (V364I)

Ref Sequence

ENSEMBL: ENSMUSP00000107614 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047830] [ENSMUST00000053932] [ENSMUST00000111982] [ENSMUST00000111983] [ENSMUST00000140666] [ENSMUST00000144544]

AlphaFold

P09027

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047830
AA Change: V364I

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000044809
Gene: ENSMUSG00000079277
AA Change: V364I

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

probably benign
Transcript: ENSMUST00000053932

SMART Domains

Protein: ENSMUSP00000051355
Gene: ENSMUSG00000100642

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: ENSMUST00000100000

Predicted Effect

possibly damaging
Transcript: ENSMUST00000111982
AA Change: V364I

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000107613
Gene: ENSMUSG00000079277
AA Change: V364I

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

possibly damaging
Transcript: ENSMUST00000111983
AA Change: V364I

PolyPhen 2 Score 0.875 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277
AA Change: V364I

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

probably benign
Transcript: ENSMUST00000140666

SMART Domains

Protein: ENSMUSP00000134616
Gene: ENSMUSG00000079277

Domain	Start	End	E-Value	Type
HOX	35	97	5.83e-28	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000144544

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152462

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000190553

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230341

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230540

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230511

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229136

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230704

Meta Mutation Damage Score

0.1013

Coding Region Coverage

1x: 99.1%
3x: 98.3%
10x: 96.4%
20x: 92.8%

Validation Efficiency

97% (95/98)

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 the regulation of cell adhesion processes. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a knock-out allele show partial postnatal lethality, asymmetric rib-sternum attachment, and anterior transformations of the cervical vertebrae I (atlas) and II (axis). Mice homozygous for a different knock-out allele lack the anteriorarch of the atlas and the dens of the axis. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 92 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
A730015C16Rik	C	A	4: 108,705,262 (GRCm39)		probably benign	Het
Actr1b	T	C	1: 36,739,173 (GRCm39)	H372R	probably benign	Het
Ampd2	C	A	3: 107,986,865 (GRCm39)		probably benign	Het
Anapc4	A	G	5: 53,020,936 (GRCm39)	S612G	probably benign	Het
Arhgef7	T	C	8: 11,850,811 (GRCm39)	L141P	probably damaging	Het
Atl1	A	G	12: 70,006,107 (GRCm39)	D471G	probably damaging	Het
Atrn	A	G	2: 130,787,939 (GRCm39)	D247G	probably benign	Het
Bag1	T	A	4: 40,948,022 (GRCm39)	R61W	probably damaging	Het
Card10	C	T	15: 78,662,451 (GRCm39)	R898H	probably damaging	Het
Cct6b	G	A	11: 82,655,046 (GRCm39)	A3V	probably damaging	Het
Cfap54	A	T	10: 92,770,953 (GRCm39)	L2097*	probably null	Het
Cfap54	T	C	10: 92,880,885 (GRCm39)		probably null	Het
Chd5	T	C	4: 152,456,554 (GRCm39)	F964L	probably benign	Het
Cog5	A	G	12: 31,936,204 (GRCm39)	T584A	probably benign	Het
Cpa2	T	A	6: 30,547,196 (GRCm39)	N157K	probably damaging	Het
Cpeb1	A	T	7: 81,001,587 (GRCm39)	M440K	probably damaging	Het
Cracr2a	G	A	6: 127,580,992 (GRCm39)	C56Y	probably damaging	Het
Ddb2	A	C	2: 91,067,073 (GRCm39)	L30R	probably damaging	Het
Dlk1	T	A	12: 109,425,697 (GRCm39)	I190N	probably damaging	Het
Dnaaf4	T	C	9: 72,879,362 (GRCm39)		probably null	Het
Dnajc13	T	A	9: 104,080,528 (GRCm39)	Y851F	possibly damaging	Het
Dop1a	T	A	9: 86,397,381 (GRCm39)	L895Q	probably damaging	Het
F7	G	A	8: 13,080,763 (GRCm39)	C122Y	probably damaging	Het
Frrs1	T	C	3: 116,696,749 (GRCm39)	V573A	possibly damaging	Het
Galnt2l	T	C	8: 122,997,175 (GRCm39)		probably benign	Het
Gm17541	A	T	12: 4,739,672 (GRCm39)		probably benign	Het
Gm5519	A	T	19: 33,800,576 (GRCm39)	H90L	probably damaging	Het
Gm5526	T	A	1: 45,896,569 (GRCm39)		noncoding transcript	Het
Gm5709	A	T	3: 59,509,971 (GRCm39)		noncoding transcript	Het
Golga4	T	A	9: 118,385,569 (GRCm39)	V869D	possibly damaging	Het
Grm7	A	T	6: 111,335,182 (GRCm39)	Q531L	probably benign	Het
Hnrnpu	C	A	1: 178,163,458 (GRCm39)	C265F	unknown	Het
Hspb8	T	C	5: 116,547,532 (GRCm39)	D150G	probably damaging	Het
Hydin	C	A	8: 111,313,855 (GRCm39)	N4244K	possibly damaging	Het
Ik	A	G	18: 36,881,926 (GRCm39)	D136G	probably benign	Het
Il11ra1	T	C	4: 41,767,932 (GRCm39)		probably benign	Het
Jph1	T	C	1: 17,161,622 (GRCm39)	I347V	probably benign	Het
Klk1	T	A	7: 43,870,985 (GRCm39)		probably benign	Het
Lmcd1	T	A	6: 112,265,087 (GRCm39)		probably benign	Het
Lnx1	C	T	5: 74,846,315 (GRCm39)	C45Y	probably damaging	Het
Macc1	T	A	12: 119,410,264 (GRCm39)	M344K	possibly damaging	Het
Madcam1	A	G	10: 79,500,779 (GRCm39)	E32G	possibly damaging	Het
Mat2a	T	C	6: 72,411,316 (GRCm39)	D383G	probably benign	Het
Mpst	T	A	15: 78,297,849 (GRCm39)	I289N	probably damaging	Het
Myh6	C	T	14: 55,190,118 (GRCm39)	R1055Q	probably damaging	Het
Myh7	T	C	14: 55,216,965 (GRCm39)	K1131E	probably damaging	Het
Ndrg3	A	T	2: 156,773,125 (GRCm39)		probably benign	Het
Nebl	A	G	2: 17,438,786 (GRCm39)	S209P	probably benign	Het
Nid2	A	G	14: 19,818,276 (GRCm39)		probably null	Het
Nup188	A	T	2: 30,220,761 (GRCm39)	S945C	probably damaging	Het
Or1j21	A	G	2: 36,683,685 (GRCm39)	M146V	probably benign	Het
Or5g23	C	T	2: 85,438,817 (GRCm39)	V146I	probably benign	Het
Or8c11	A	G	9: 38,289,213 (GRCm39)	N12S	probably benign	Het
Otx1	C	A	11: 21,947,037 (GRCm39)	A91S	probably damaging	Het
Patl2	A	G	2: 121,959,368 (GRCm39)	L32P	probably damaging	Het
Pcdh20	T	A	14: 88,705,813 (GRCm39)	M496L	probably benign	Het
Pdzd2	A	G	15: 12,373,028 (GRCm39)	V2369A	possibly damaging	Het
Pfn2	A	G	3: 57,754,812 (GRCm39)	V31A	probably damaging	Het
Plxna4	T	C	6: 32,228,007 (GRCm39)	N533S	probably benign	Het
Plxnb1	T	C	9: 108,943,661 (GRCm39)	F1916S	probably damaging	Het
Ppp4r3b	T	C	11: 29,138,293 (GRCm39)	F214L	probably benign	Het
Prox1	T	C	1: 189,893,638 (GRCm39)	D269G	probably benign	Het
Rapgef4	T	C	2: 71,864,378 (GRCm39)	F71S	probably damaging	Het
Rft1	A	G	14: 30,383,243 (GRCm39)	I94M	probably benign	Het
S100z	T	C	13: 95,615,127 (GRCm39)	I13V	probably damaging	Het
Serhl	T	A	15: 82,986,835 (GRCm39)	V117E	probably damaging	Het
Shroom1	G	A	11: 53,356,334 (GRCm39)	R336Q	probably benign	Het
Sik3	A	T	9: 46,123,552 (GRCm39)	Q1067L	probably damaging	Het
Slc22a30	G	A	19: 8,321,757 (GRCm39)	Q436*	probably null	Het
Slc28a1	G	A	7: 80,771,869 (GRCm39)	V118M	probably damaging	Het
Slco1a6	T	A	6: 142,078,427 (GRCm39)	I153F	probably benign	Het
Ss18l1	T	C	2: 179,703,735 (GRCm39)	Y323H	unknown	Het
Susd4	G	T	1: 182,719,824 (GRCm39)	A480S	possibly damaging	Het
Syne3	A	T	12: 104,942,139 (GRCm39)	M1K	probably null	Het
Synpo2l	A	T	14: 20,711,082 (GRCm39)	S513T	probably benign	Het
Tat	A	T	8: 110,724,966 (GRCm39)	N388I	probably benign	Het
Tbc1d1	A	G	5: 64,439,352 (GRCm39)	Y619C	probably damaging	Het
Tbk1	G	A	10: 121,406,590 (GRCm39)	T216M	probably damaging	Het
Tns1	C	T	1: 74,034,585 (GRCm39)		probably benign	Het
Trbv5	T	C	6: 41,039,318 (GRCm39)	V9A	possibly damaging	Het
Trpm5	A	G	7: 142,636,040 (GRCm39)	Y575H	probably damaging	Het
Ttn	A	T	2: 76,570,045 (GRCm39)	Y25203*	probably null	Het
Tubb3	C	A	8: 124,148,391 (GRCm39)	D441E	probably benign	Het
Usp33	T	A	3: 152,097,333 (GRCm39)	C850*	probably null	Het
Vdac1	G	A	11: 52,274,905 (GRCm39)		probably null	Het
Vmn1r232	T	C	17: 21,133,846 (GRCm39)	I251M	probably damaging	Het
Vmn2r11	T	G	5: 109,202,658 (GRCm39)	I140L	probably benign	Het
Vmn2r6	A	T	3: 64,464,263 (GRCm39)	N190K	probably benign	Het
Vps51	T	A	19: 6,120,518 (GRCm39)	H465L	probably benign	Het
Zfp318	T	G	17: 46,722,995 (GRCm39)	I1666S	probably benign	Het
Zfp446	C	T	7: 12,713,231 (GRCm39)	R90*	probably null	Het
Zgrf1	T	A	3: 127,396,094 (GRCm39)	F547I	probably damaging	Het

Other mutations in Hoxd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02636:Hoxd3	APN	2	74,577,298 (GRCm39)	missense	probably benign	0.32
IGL03017:Hoxd3	APN	2	74,577,050 (GRCm39)	missense	possibly damaging	0.68
candide	UTSW	2	74,574,420 (GRCm39)	missense	probably damaging	1.00
compressed	UTSW	2	74,574,650 (GRCm39)	nonsense	probably null
R1977:Hoxd3	UTSW	2	74,574,620 (GRCm39)	missense	possibly damaging	0.94
R2079:Hoxd3	UTSW	2	74,574,610 (GRCm39)	missense	probably damaging	0.97
R2124:Hoxd3	UTSW	2	74,574,578 (GRCm39)	missense	possibly damaging	0.92
R5143:Hoxd3	UTSW	2	74,576,716 (GRCm39)	missense	probably damaging	1.00
R5250:Hoxd3	UTSW	2	74,574,650 (GRCm39)	nonsense	probably null
R5943:Hoxd3	UTSW	2	74,577,173 (GRCm39)	missense	probably benign	0.00
R6300:Hoxd3	UTSW	2	74,574,420 (GRCm39)	missense	probably damaging	1.00
R7362:Hoxd3	UTSW	2	74,574,563 (GRCm39)	missense	possibly damaging	0.59
R9203:Hoxd3	UTSW	2	74,576,744 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- AATCGCAGCCCAATATGTACGG -3'
(R):5'- AGAGAGGTAATTGCGCCTG -3'

Sequencing Primer
(F):5'- AGCCCAATATGTACGGCCTGG -3'
(R):5'- CAACAGCTACAGATGTGTCAGTTTGG -3'

Posted On

2016-07-06