Mutagenetix > Incidental Mutation

Incidental Mutation 'IGL02636:Hoxd3'

301509

Institutional Source

Australian Phenomics Network (link to record)

Gene Symbol

Hoxd3

Ensembl Gene

ENSMUSG00000079277

Gene Name

homeobox D3

Synonyms

Hox-5.5, Hox-4.1

Accession Numbers

Essential gene?

Probably essential (E-score: 0.823) question?

Stock #

IGL02636

Quality Score

Status

Chromosome

Chromosomal Location

74542337-74578615 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

G to A at 74577298 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Threonine at position 393 (A393T)

Ref Sequence

ENSEMBL: ENSMUSP00000107614 (fasta)

Gene Model

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

AlphaFold

P09027

Predicted Effect

probably benign
Transcript: ENSMUST00000047830
AA Change: A393T

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000044809
Gene: ENSMUSG00000079277
AA Change: A393T

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

probably benign
Transcript: ENSMUST00000111982
AA Change: A393T

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107613
Gene: ENSMUSG00000079277
AA Change: A393T

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: ENSMUST00000111983
AA Change: A393T

PolyPhen 2 Score 0.319 (Sensitivity: 0.90; Specificity: 0.89)

SMART Domains

Protein: ENSMUSP00000107614
Gene: ENSMUSG00000079277
AA Change: A393T

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: ENSMUST00000230540

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230341

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000229136

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230511

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000230704

Coding Region Coverage

Validation Efficiency

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: 32 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Alms1	C	A	6: 85,605,636 (GRCm39)	Q1960K	probably benign	Het
Arhgef40	T	A	14: 52,234,865 (GRCm39)	V1056E	probably damaging	Het
Cdh26	T	A	2: 178,091,755 (GRCm39)	F105I	probably damaging	Het
Cep162	A	T	9: 87,130,432 (GRCm39)	D59E	possibly damaging	Het
Cngb3	A	T	4: 19,396,690 (GRCm39)	T348S	probably damaging	Het
Eci3	A	T	13: 35,130,963 (GRCm39)		probably null	Het
Gapvd1	A	G	2: 34,615,416 (GRCm39)	I409T	probably benign	Het
Golga2	T	C	2: 32,186,735 (GRCm39)		probably null	Het
Htr5a	T	C	5: 28,047,658 (GRCm39)	F71S	probably damaging	Het
Hyou1	T	C	9: 44,292,707 (GRCm39)		probably null	Het
Igsf6	C	A	7: 120,666,503 (GRCm39)		probably benign	Het
Klrb1c	C	A	6: 128,765,515 (GRCm39)	C25F	probably benign	Het
Lrguk	C	A	6: 34,067,123 (GRCm39)	T483K	probably damaging	Het
Lrpprc	A	T	17: 85,060,532 (GRCm39)		probably benign	Het
Lrrk1	A	T	7: 65,958,407 (GRCm39)		probably null	Het
Megf8	G	A	7: 25,057,857 (GRCm39)	G2098D	probably damaging	Het
Nfkbia	T	C	12: 55,537,958 (GRCm39)	Q165R	possibly damaging	Het
Nipsnap2	A	G	5: 129,822,354 (GRCm39)		probably benign	Het
Phykpl	C	T	11: 51,489,540 (GRCm39)	T382I	probably damaging	Het
Prdm10	A	G	9: 31,240,977 (GRCm39)	D206G	possibly damaging	Het
Rab26	T	C	17: 24,752,533 (GRCm39)	S9G	probably benign	Het
Sema3e	C	A	5: 14,275,670 (GRCm39)	N258K	probably benign	Het
Slfn10-ps	T	A	11: 82,920,971 (GRCm39)		noncoding transcript	Het
Tgm5	A	T	2: 120,907,277 (GRCm39)	C149S	probably damaging	Het
Timp4	C	T	6: 115,226,785 (GRCm39)		probably null	Het
Traf7	T	C	17: 24,731,964 (GRCm39)	K251E	probably benign	Het
Ugcg	G	T	4: 59,207,763 (GRCm39)	R34L	possibly damaging	Het
Unc13d	T	C	11: 115,964,444 (GRCm39)	H300R	probably damaging	Het
Vmn1r20	G	T	6: 57,408,746 (GRCm39)	C24F	probably benign	Het
Vmn2r13	T	C	5: 109,339,883 (GRCm39)	R31G	probably damaging	Het
Vsig10l	A	G	7: 43,113,002 (GRCm39)	T87A	possibly damaging	Het
Zfp353-ps	T	A	8: 42,535,477 (GRCm39)		noncoding transcript	Het

Other mutations in Hoxd3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
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
R5256:Hoxd3	UTSW	2	74,577,211 (GRCm39)	missense	possibly damaging	0.88
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

Posted On

2015-04-16