Mutagenetix > Incidental Mutation

Incidental Mutation 'R6197:Hoxd4'

502960

Institutional Source

Beutler Lab

Gene Symbol

Hoxd4

Ensembl Gene

ENSMUSG00000101174

Gene Name

homeobox D4

Synonyms

Hox-5.1, Hox-4.2

MMRRC Submission

044337-MU

Accession Numbers

Essential gene?

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

Stock #

R6197 (G1)

Quality Score

225.009

Status

Validated

Chromosome

Chromosomal Location

74552322-74559504 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 74558807 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 210 (D210G)

Ref Sequence

ENSEMBL: ENSMUSP00000107611 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000047904] [ENSMUST00000053932] [ENSMUST00000111980] [ENSMUST00000111983] [ENSMUST00000144544]

AlphaFold

P10628

Predicted Effect

possibly damaging
Transcript: ENSMUST00000047904
AA Change: D210G

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000047949
Gene: ENSMUSG00000115956
AA Change: D210G

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: 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: ENSMUST00000083566

Predicted Effect

possibly damaging
Transcript: ENSMUST00000111980
AA Change: D210G

PolyPhen 2 Score 0.845 (Sensitivity: 0.83; Specificity: 0.93)

SMART Domains

Protein: ENSMUSP00000107611
Gene: ENSMUSG00000101174
AA Change: D210G

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

Predicted Effect

probably benign
Transcript: ENSMUST00000144544

Coding Region Coverage

1x: 100.0%
3x: 99.9%
10x: 99.6%
20x: 98.7%

Validation Efficiency

92% (49/53)

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: 54 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
1700109H08Rik	T	A	5: 3,630,442 (GRCm39)	Y119*	probably null	Het
Abcb9	C	A	5: 124,209,812 (GRCm39)	E664*	probably null	Het
Adgrl2	T	C	3: 148,564,578 (GRCm39)	D334G	probably damaging	Het
Ak9	T	G	10: 41,193,826 (GRCm39)	C57G	probably damaging	Het
Als2cl	A	G	9: 110,724,952 (GRCm39)	K809E	probably damaging	Het
Arsi	G	A	18: 61,049,723 (GRCm39)	G202E	probably benign	Het
Atp11a	A	G	8: 12,896,099 (GRCm39)	I223V	probably benign	Het
Cacna2d3	A	T	14: 28,630,278 (GRCm39)	V1022E	probably benign	Het
Cc2d1b	C	T	4: 108,490,422 (GRCm39)	R825W	probably damaging	Het
Cd37	A	G	7: 44,886,598 (GRCm39)	C85R	probably damaging	Het
Ces1g	T	C	8: 94,063,764 (GRCm39)	S7G	probably benign	Het
Cltc	T	C	11: 86,611,188 (GRCm39)	N561S	probably benign	Het
Cnbd2	A	G	2: 156,217,494 (GRCm39)	E661G	possibly damaging	Het
Col6a3	A	T	1: 90,750,063 (GRCm39)	F257Y	probably damaging	Het
Cpt1b	T	C	15: 89,309,037 (GRCm39)	Y55C	possibly damaging	Het
Csmd1	A	G	8: 15,976,611 (GRCm39)	V2869A	probably benign	Het
Dnah11	T	C	12: 118,143,482 (GRCm39)	E387G	probably benign	Het
Eny2	T	A	15: 44,292,949 (GRCm39)		probably null	Het
Fbxo10	G	T	4: 45,043,857 (GRCm39)	H655Q	probably benign	Het
Gm14403	AAACCCTA	AA	2: 177,201,448 (GRCm39)		probably benign	Het
Gpx2	C	T	12: 76,842,068 (GRCm39)	G28S	probably damaging	Het
H2-Q5	G	T	17: 35,613,918 (GRCm39)	A156S	probably benign	Het
Hoxd9	A	G	2: 74,529,166 (GRCm39)	Q256R	probably damaging	Het
Macf1	A	G	4: 123,346,085 (GRCm39)	V2571A	probably damaging	Het
Mtus1	A	G	8: 41,537,074 (GRCm39)	V214A	possibly damaging	Het
Myh1	C	T	11: 67,111,793 (GRCm39)	A1716V	probably benign	Het
Nbeal1	A	G	1: 60,261,287 (GRCm39)	D249G	probably damaging	Het
Nup54	TCTGCTGCTGCTGCTGCTGCTGCTG	TCTGCTGCTGCTGCTGCTGCTG	5: 92,578,663 (GRCm39)		probably benign	Het
Or10v9	G	T	19: 11,833,148 (GRCm39)	H56Q	probably damaging	Het
Or4c124	A	T	2: 89,155,677 (GRCm39)	N282K	probably damaging	Het
Or5w17	C	T	2: 87,583,696 (GRCm39)	V214I	probably benign	Het
Or7a37	T	G	10: 78,805,974 (GRCm39)	L164V	probably damaging	Het
Peg10	GC	GCTCC	6: 4,756,452 (GRCm39)		probably benign	Het
Pramel23	T	C	4: 143,423,886 (GRCm39)	Y301C	possibly damaging	Het
Prss59	A	G	6: 40,897,939 (GRCm39)	I248T	probably benign	Het
Pwwp2a	A	G	11: 43,595,423 (GRCm39)	D196G	probably benign	Het
Rarg	A	T	15: 102,150,327 (GRCm39)	C93S	possibly damaging	Het
Rcc1	T	C	4: 132,065,073 (GRCm39)	D150G	possibly damaging	Het
Ripk2	A	G	4: 16,163,330 (GRCm39)	Y23H	probably damaging	Het
Rragc	A	G	4: 123,811,340 (GRCm39)	Y5C	possibly damaging	Het
Rubcnl	G	A	14: 75,269,369 (GRCm39)	G9D	probably damaging	Het
Sephs2	A	T	7: 126,872,073 (GRCm39)	V340E	probably damaging	Het
Slc22a3	C	T	17: 12,677,438 (GRCm39)	M243I	probably benign	Het
Slco6c1	A	G	1: 97,000,518 (GRCm39)		probably null	Het
Sncaip	T	G	18: 53,039,966 (GRCm39)	I308R	probably damaging	Het
Supt16	G	A	14: 52,408,338 (GRCm39)	T869M	probably damaging	Het
Tanc1	G	A	2: 59,674,366 (GRCm39)	E1817K	possibly damaging	Het
Usp4	C	A	9: 108,248,154 (GRCm39)	Q395K	probably damaging	Het
Usp49	T	A	17: 47,984,272 (GRCm39)	S210T	possibly damaging	Het
Virma	A	G	4: 11,505,498 (GRCm39)	I124M	probably damaging	Het
Vmn1r234	G	A	17: 21,449,589 (GRCm39)	V168I	probably benign	Het
Vnn3	T	A	10: 23,732,187 (GRCm39)	C146S	probably damaging	Het
Ylpm1	A	G	12: 85,088,953 (GRCm39)	D1234G	probably damaging	Het
Zfp617	T	A	8: 72,687,098 (GRCm39)	V476E	probably benign	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
R5447:Hoxd4	UTSW	2	74,557,687 (GRCm39)	missense	probably damaging	1.00
R5715:Hoxd4	UTSW	2	74,557,708 (GRCm39)	missense	probably damaging	1.00
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'- TGTCTCATAGTGAACCCCAAC -3'
(R):5'- TTAGAGCCCAGTGAGGTGACAG -3'

Sequencing Primer
(F):5'- TGTCTCATAGTGAACCCCAACTACAC -3'
(R):5'- TGAGGTGACAGCAGGCC -3'

Posted On

2018-02-27