Mutagenetix > Incidental Mutation

Incidental Mutation 'R6248:Hoxd9'

527950

Institutional Source

Beutler Lab

Gene Symbol

Hoxd9

Ensembl Gene

ENSMUSG00000043342

Gene Name

homeobox D9

Synonyms

Hox-5.2, Hox-4.4

Accession Numbers

Essential gene?

Non essential (E-score: 0.000) question?

Stock #

R6248 (G1)

Quality Score

50.0072

Status

Validated

Chromosome

Chromosomal Location

74528107-74530552 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 74528980 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glutamic Acid to Glycine at position 194 (E194G)

Ref Sequence

ENSEMBL: ENSMUSP00000058490 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000059272] [ENSMUST00000061745]

AlphaFold

P28357

Predicted Effect

probably benign
Transcript: ENSMUST00000059272
AA Change: E194G

PolyPhen 2 Score 0.087 (Sensitivity: 0.93; Specificity: 0.85)

SMART Domains

Protein: ENSMUSP00000058490
Gene: ENSMUSG00000043342
AA Change: E194G

Domain	Start	End	E-Value	Type
Pfam:Hox9_act	1	126	2e-47	PFAM
low complexity region	155	176	N/A	INTRINSIC
low complexity region	208	225	N/A	INTRINSIC
low complexity region	248	256	N/A	INTRINSIC
HOX	272	334	6.25e-28	SMART

Predicted Effect

probably benign
Transcript: ENSMUST00000061745

SMART Domains

Protein: ENSMUSP00000062412
Gene: ENSMUSG00000050368

Domain	Start	End	E-Value	Type
low complexity region	24	43	N/A	INTRINSIC
HOX	266	328	3.3e-27	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000126966

SMART Domains

Protein: ENSMUSP00000133930
Gene: ENSMUSG00000086077

Domain	Start	End	E-Value	Type
low complexity region	23	42	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000132326

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000136302

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000152027

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000190845

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000198895

Coding Region Coverage

1x: 99.9%
3x: 99.6%
10x: 98.0%
20x: 94.2%

Validation Efficiency

100% (92/92)

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 exact role of this gene has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Mice homozygous for a targeted mutation exhibit anterior transformation of lumbar, sacral, and caudal vertebrae with abnormal humerus morphology. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 93 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4930523C07Rik	T	C	1: 159,902,978 (GRCm39)	S83P	possibly damaging	Het
Actr10	A	T	12: 70,999,733 (GRCm39)	E176D	probably benign	Het
Adcy3	G	A	12: 4,258,662 (GRCm39)		probably null	Het
AI429214	T	A	8: 37,461,278 (GRCm39)	I142N	probably damaging	Het
Alox12	A	G	11: 70,143,936 (GRCm39)	L148S	probably damaging	Het
Ank3	A	G	10: 69,809,680 (GRCm39)	I1147V	probably benign	Het
Apoc2	C	T	7: 19,407,493 (GRCm39)	V12I	probably benign	Het
Arap3	T	C	18: 38,124,407 (GRCm39)	S311G	probably benign	Het
Arih2	G	T	9: 108,488,841 (GRCm39)	H292Q	probably damaging	Het
Cdc14a	A	T	3: 116,101,843 (GRCm39)	D312E	probably benign	Het
Cdh12	T	G	15: 21,237,800 (GRCm39)	W12G	possibly damaging	Het
Cisd2	A	T	3: 135,114,616 (GRCm39)	N118K	probably damaging	Het
Cntnap5b	A	G	1: 99,999,827 (GRCm39)	Q195R	probably benign	Het
Cyp2r1	A	G	7: 114,161,966 (GRCm39)		probably null	Het
Cyp4f37	A	G	17: 32,848,864 (GRCm39)	D244G	possibly damaging	Het
Dab1	C	T	4: 104,588,948 (GRCm39)	A524V	probably benign	Het
Dido1	T	A	2: 180,302,048 (GRCm39)	H1952L	probably damaging	Het
Dnah10	T	A	5: 124,871,283 (GRCm39)		probably null	Het
Dnal4	T	A	15: 79,646,714 (GRCm39)	M56L	probably damaging	Het
Emilin2	A	G	17: 71,581,112 (GRCm39)	V538A	probably benign	Het
Eps8l2	A	G	7: 140,922,015 (GRCm39)	D31G	probably damaging	Het
Erp44	A	T	4: 48,219,479 (GRCm39)	L112*	probably null	Het
Etl4	C	T	2: 20,813,900 (GRCm39)	T1907I	possibly damaging	Het
Exoc3	A	G	13: 74,330,400 (GRCm39)	F510L	probably benign	Het
Fam114a2	G	T	11: 57,383,942 (GRCm39)	T324K	possibly damaging	Het
Fer1l4	G	A	2: 155,888,091 (GRCm39)	R465C	probably damaging	Het
Frmd4b	A	C	6: 97,436,173 (GRCm39)	S2R	probably benign	Het
Fscn1	A	T	5: 142,946,778 (GRCm39)	D192V	possibly damaging	Het
Gm3486	T	A	14: 41,206,472 (GRCm39)	*200C	probably null	Het
Gusb	A	T	5: 130,029,366 (GRCm39)	H138Q	probably benign	Het
Hdac9	A	T	12: 34,578,293 (GRCm39)	M4K	possibly damaging	Het
Hhipl1	G	T	12: 108,284,964 (GRCm39)	R439L	probably benign	Het
Itgb1	A	G	8: 129,448,902 (GRCm39)	S503G	possibly damaging	Het
Kcnt2	T	A	1: 140,437,216 (GRCm39)	C500S	probably damaging	Het
Kdm7a	G	A	6: 39,123,983 (GRCm39)	S727L	possibly damaging	Het
Klhdc4	A	G	8: 122,540,507 (GRCm39)	F92L	probably damaging	Het
Klrb1a	A	G	6: 128,596,137 (GRCm39)	V62A	probably damaging	Het
Krit1	A	G	5: 3,863,032 (GRCm39)		probably null	Het
Krt40	A	G	11: 99,432,566 (GRCm39)	I150T	possibly damaging	Het
Larp4b	A	G	13: 9,208,738 (GRCm39)	T464A	probably benign	Het
Lrrc52	T	G	1: 167,293,964 (GRCm39)	D107A	probably damaging	Het
Mapkap1	G	T	2: 34,408,692 (GRCm39)	V35F	probably damaging	Het
Mccc1	A	G	3: 36,044,313 (GRCm39)	V171A	probably damaging	Het
Metap1d	A	T	2: 71,346,104 (GRCm39)	R222*	probably null	Het
Mrgpre	G	A	7: 143,334,603 (GRCm39)	A300V	probably benign	Het
Mterf1b	C	A	5: 4,246,606 (GRCm39)	N82K	probably benign	Het
Myh9	C	T	15: 77,669,422 (GRCm39)	W533*	probably null	Het
Myom2	A	G	8: 15,148,472 (GRCm39)		probably null	Het
Ncor1	G	A	11: 62,257,808 (GRCm39)	P329S	probably damaging	Het
Nr2f1	T	C	13: 78,344,611 (GRCm39)		probably benign	Het
Or10x1	T	G	1: 174,197,236 (GRCm39)	V251G	probably benign	Het
Or11a4	T	A	17: 37,536,451 (GRCm39)	L145*	probably null	Het
Or2a57	C	T	6: 43,212,838 (GRCm39)	Q99*	probably null	Het
Or2w6	A	T	13: 21,843,244 (GRCm39)	I83N	possibly damaging	Het
Or52p2	T	C	7: 102,237,237 (GRCm39)	T238A	probably benign	Het
Or6c210	A	G	10: 129,496,532 (GRCm39)	I286V	probably benign	Het
Or6z1	A	T	7: 6,504,675 (GRCm39)	C183*	probably null	Het
Pcdha11	T	C	18: 37,138,950 (GRCm39)	L193P	probably benign	Het
Pcdhb20	T	A	18: 37,639,285 (GRCm39)	F604I	probably damaging	Het
Pde1a	T	C	2: 79,708,545 (GRCm39)	H291R	probably damaging	Het
Pfkm	G	A	15: 98,024,260 (GRCm39)	V423M	probably damaging	Het
Pira1	C	A	7: 3,739,337 (GRCm39)	E510D	probably benign	Het
Pkd2l1	G	T	19: 44,146,108 (GRCm39)	Q149K	probably benign	Het
Pkhd1l1	T	A	15: 44,392,955 (GRCm39)	N1763K	probably benign	Het
Pla2g4a	G	A	1: 149,748,338 (GRCm39)	T282I	probably damaging	Het
Prpf39	A	C	12: 65,089,528 (GRCm39)	N89H	probably damaging	Het
Rad54l2	A	G	9: 106,587,537 (GRCm39)	F743L	probably damaging	Het
Raver2	A	G	4: 100,991,320 (GRCm39)		probably null	Het
Ric8b	T	C	10: 84,783,709 (GRCm39)	L189P	probably damaging	Het
Sccpdh	T	C	1: 179,495,957 (GRCm39)	F13L	probably benign	Het
Scd2	T	C	19: 44,291,448 (GRCm39)	F296L	probably damaging	Het
Scg2	G	T	1: 79,414,023 (GRCm39)	D233E	probably benign	Het
Sema5b	C	A	16: 35,448,377 (GRCm39)		probably null	Het
Skint5	A	T	4: 113,636,286 (GRCm39)	V644E	unknown	Het
Slc44a5	G	T	3: 153,969,678 (GRCm39)	V612F	possibly damaging	Het
Snd1	C	T	6: 28,520,234 (GRCm39)	R107*	probably null	Het
Sun5	G	T	2: 153,702,589 (GRCm39)	T189K	probably damaging	Het
Tap1	A	T	17: 34,412,151 (GRCm39)	E452V	probably damaging	Het
Tcam1	A	G	11: 106,173,652 (GRCm39)	N32S	probably benign	Het
Tep1	T	C	14: 51,067,715 (GRCm39)	E2167G	probably damaging	Het
Tm9sf1	C	T	14: 55,873,827 (GRCm39)	R557H	probably damaging	Het
Tmem175	T	C	5: 108,793,821 (GRCm39)	V317A	probably damaging	Het
Tsga13	A	G	6: 30,874,139 (GRCm39)	V231A	probably benign	Het
Tspan12	A	G	6: 21,799,970 (GRCm39)	S126P	probably damaging	Het
Uvrag	G	T	7: 98,637,398 (GRCm39)	D143E	probably damaging	Het
Vmn1r230	T	A	17: 21,067,036 (GRCm39)	M75K	possibly damaging	Het
Vmn2r120	A	T	17: 57,852,287 (GRCm39)	F10I	probably benign	Het
Vmn2r57	T	C	7: 41,049,284 (GRCm39)	T822A	probably benign	Het
Vmn2r67	T	C	7: 84,799,768 (GRCm39)	Y490C	probably damaging	Het
Zc3h7b	T	A	15: 81,667,386 (GRCm39)	W644R	probably damaging	Het
Zeb1	A	G	18: 5,766,962 (GRCm39)	D491G	probably damaging	Het
Zfp709	TCGACG	TCG	8: 72,644,552 (GRCm39)		probably benign	Het
Zfp831	A	T	2: 174,486,308 (GRCm39)	T328S	possibly damaging	Het

Other mutations in Hoxd9

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
R0723:Hoxd9	UTSW	2	74,529,172 (GRCm39)	missense	probably damaging	1.00
R3743:Hoxd9	UTSW	2	74,528,710 (GRCm39)	missense	probably damaging	0.99
R4155:Hoxd9	UTSW	2	74,529,667 (GRCm39)	missense	probably benign	0.15
R4261:Hoxd9	UTSW	2	74,526,031 (GRCm39)	unclassified	probably benign
R5794:Hoxd9	UTSW	2	74,529,617 (GRCm39)	missense	probably damaging	1.00
R6114:Hoxd9	UTSW	2	74,529,709 (GRCm39)	missense	probably damaging	1.00
R6197:Hoxd9	UTSW	2	74,529,166 (GRCm39)	missense	probably damaging	0.99
R6268:Hoxd9	UTSW	2	74,528,433 (GRCm39)	missense	probably damaging	1.00
R6717:Hoxd9	UTSW	2	74,528,733 (GRCm39)	missense	probably benign	0.01
R6809:Hoxd9	UTSW	2	74,529,590 (GRCm39)	missense	probably damaging	1.00
R7183:Hoxd9	UTSW	2	74,528,709 (GRCm39)	missense	possibly damaging	0.59
R7254:Hoxd9	UTSW	2	74,528,718 (GRCm39)	missense	probably damaging	1.00
R9160:Hoxd9	UTSW	2	74,529,761 (GRCm39)	missense	unknown
R9277:Hoxd9	UTSW	2	74,529,539 (GRCm39)	missense	possibly damaging	0.76
R9445:Hoxd9	UTSW	2	74,528,415 (GRCm39)	missense	probably damaging	0.99
Z1176:Hoxd9	UTSW	2	74,528,472 (GRCm39)	missense	probably damaging	0.99
Z1177:Hoxd9	UTSW	2	74,528,869 (GRCm39)	missense	probably benign	0.04

Predicted Primers

PCR Primer
(F):5'- CAAATCGTCCGTGTTCTCCG -3'
(R):5'- TCTTTTGCACTTACTTGGGTCAAG -3'

Sequencing Primer
(F):5'- TACGTACGCTCCTGGATGG -3'
(R):5'- TCAAGTTGCTGCTGCGGC -3'

Posted On

2018-07-23