Mutagenetix > Incidental Mutation

Incidental Mutation 'R5093:Hdgfl2'

387968

Institutional Source

Beutler Lab

Gene Symbol

Hdgfl2

Ensembl Gene

ENSMUSG00000002833

Gene Name

HDGF like 2

Synonyms

HRP-2, Hdgfrp2

MMRRC Submission

042682-MU

Accession Numbers

Essential gene?

Probably non essential (E-score: 0.146) question?

Stock #

R5093 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

56386634-56407607 bp(+) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 56406217 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Alanine to Valine at position 535 (A535V)

Ref Sequence

ENSEMBL: ENSMUSP00000152948 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002908] [ENSMUST00000002911] [ENSMUST00000190703] [ENSMUST00000225843] [ENSMUST00000226053]

AlphaFold

Q3UMU9

Predicted Effect

probably benign
Transcript: ENSMUST00000002908

SMART Domains

Protein: ENSMUSP00000002908
Gene: ENSMUSG00000002831

Domain	Start	End	E-Value	Type
low complexity region	19	31	N/A	INTRINSIC
internal_repeat_2	74	335	9.44e-7	PROSPERO
internal_repeat_1	103	467	2.72e-12	PROSPERO
internal_repeat_2	343	701	9.44e-7	PROSPERO
internal_repeat_1	598	1090	2.72e-12	PROSPERO
low complexity region	1124	1136	N/A	INTRINSIC
Pfam:Perilipin	1144	1385	2.3e-22	PFAM

Predicted Effect

unknown
Transcript: ENSMUST00000002911
AA Change: A534V

SMART Domains

Protein: ENSMUSP00000002911
Gene: ENSMUSG00000002833
AA Change: A534V

Domain	Start	End	E-Value	Type
PWWP	5	62	1.78e-19	SMART
low complexity region	90	109	N/A	INTRINSIC
low complexity region	127	136	N/A	INTRINSIC
low complexity region	137	153	N/A	INTRINSIC
low complexity region	163	175	N/A	INTRINSIC
low complexity region	181	196	N/A	INTRINSIC
low complexity region	212	243	N/A	INTRINSIC
low complexity region	252	272	N/A	INTRINSIC
low complexity region	273	300	N/A	INTRINSIC
low complexity region	301	311	N/A	INTRINSIC
coiled coil region	321	364	N/A	INTRINSIC
low complexity region	398	411	N/A	INTRINSIC
Pfam:LEDGF	468	569	2.8e-31	PFAM
internal_repeat_1	575	644	2.5e-5	PROSPERO

Predicted Effect

probably benign
Transcript: ENSMUST00000190703

SMART Domains

Protein: ENSMUSP00000139859
Gene: ENSMUSG00000002831

Domain	Start	End	E-Value	Type
low complexity region	19	31	N/A	INTRINSIC
internal_repeat_2	74	335	9.44e-7	PROSPERO
internal_repeat_1	103	467	2.72e-12	PROSPERO
internal_repeat_2	343	701	9.44e-7	PROSPERO
internal_repeat_1	598	1090	2.72e-12	PROSPERO
Pfam:Perilipin	1110	1385	1.4e-16	PFAM

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224101

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224172

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224655

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000224701

Predicted Effect

possibly damaging
Transcript: ENSMUST00000225843
AA Change: A544V

PolyPhen 2 Score 0.904 (Sensitivity: 0.82; Specificity: 0.94)

Predicted Effect

possibly damaging
Transcript: ENSMUST00000226053
AA Change: A535V

PolyPhen 2 Score 0.922 (Sensitivity: 0.81; Specificity: 0.94)

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000226035

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225731

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225342

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000225208

Meta Mutation Damage Score

0.2528

Coding Region Coverage

1x: 99.2%
3x: 98.5%
10x: 96.9%
20x: 94.1%

Validation Efficiency

99% (90/91)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of the hepatoma-derived growth factor (HDGF) family. The protein includes an N-terminal PWWP domain that binds to methyl-lysine-containing histones, with specific binding of this protein to tri-methylated lysines 36 and 79 of histone H3, and di- and tri-methylated lysine 20 of histone H4. The protein functions in LEDGF/p75-independent HIV-1 replication by determining HIV-1 integration site selection. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
PHENOTYPE: Homozygous mice exhibit an increased mean serum alkaline phosphatase level compared to controls. Female mutants exhibited a decreased mean skin fibroblast proliferation rate. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 81 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4833420G17Rik	C	T	13: 119,610,573 (GRCm39)		probably benign	Het
Abca9	A	T	11: 110,032,358 (GRCm39)	L753Q	probably damaging	Het
Acvrl1	A	G	15: 101,032,628 (GRCm39)		probably null	Het
Adgrv1	A	T	13: 81,740,704 (GRCm39)	N141K	probably damaging	Het
Aftph	C	T	11: 20,659,619 (GRCm39)		probably null	Het
Aifm1	C	T	X: 47,571,637 (GRCm39)	G371S	probably benign	Het
Aldh3b2	A	G	19: 4,029,433 (GRCm39)	M269V	probably benign	Het
Ankrd44	T	C	1: 54,802,877 (GRCm39)	Y207C	probably damaging	Het
Arhgap15	G	T	2: 44,212,767 (GRCm39)	M412I	probably damaging	Het
Auts2	A	C	5: 131,468,296 (GRCm39)	L783R	probably damaging	Het
Baiap2l1	A	T	5: 144,215,363 (GRCm39)	Y381N	probably damaging	Het
Baiap3	T	C	17: 25,469,243 (GRCm39)	D180G	probably damaging	Het
Cant1	T	C	11: 118,302,038 (GRCm39)	Y93C	probably damaging	Het
Catsperg2	T	C	7: 29,416,423 (GRCm39)	S330G	probably benign	Het
Ccdc73	A	T	2: 104,848,111 (GRCm39)		probably benign	Het
Cdc5l	A	T	17: 45,703,967 (GRCm39)	F752L	possibly damaging	Het
Celsr2	G	T	3: 108,320,689 (GRCm39)	H708N	possibly damaging	Het
Cep170	T	A	1: 176,596,896 (GRCm39)	K487M	possibly damaging	Het
Cerkl	A	T	2: 79,163,867 (GRCm39)	N66K	probably damaging	Het
Cilk1	G	A	9: 78,047,303 (GRCm39)	V68I	probably benign	Het
Clec11a	C	T	7: 43,954,150 (GRCm39)	A268T	probably damaging	Het
Ctnna2	C	A	6: 77,091,912 (GRCm39)		probably null	Het
Diaph3	C	A	14: 87,222,236 (GRCm39)	R416L	probably damaging	Het
Dnmbp	T	A	19: 43,838,315 (GRCm39)	N1170I	probably damaging	Het
Erbb2	G	T	11: 98,318,279 (GRCm39)	C505F	probably damaging	Het
Ercc6	T	A	14: 32,289,479 (GRCm39)	F904L	probably damaging	Het
Exo5	C	T	4: 120,779,514 (GRCm39)	G117D	probably damaging	Het
F2	CAGAAAG	CAG	2: 91,465,302 (GRCm39)		probably benign	Het
Fbxl5	A	G	5: 43,930,896 (GRCm39)	Y64H	probably damaging	Het
Gabra4	T	A	5: 71,798,207 (GRCm39)	M207L	probably damaging	Het
Galnt15	T	C	14: 31,771,786 (GRCm39)	L277P	probably damaging	Het
Gclm	T	C	3: 122,049,261 (GRCm39)		probably null	Het
Gm5493	T	A	17: 22,966,201 (GRCm39)	C29S	possibly damaging	Het
Grik3	A	G	4: 125,564,382 (GRCm39)	T455A	probably benign	Het
Grm3	A	G	5: 9,639,766 (GRCm39)	V93A	probably benign	Het
Hfm1	A	T	5: 107,049,597 (GRCm39)	S455T	probably damaging	Het
Hmcn1	T	A	1: 150,613,007 (GRCm39)	D1424V	probably benign	Het
Hsd3b6	C	T	3: 98,715,120 (GRCm39)	V91I	probably benign	Het
Igdcc4	G	A	9: 65,030,039 (GRCm39)	S363N	possibly damaging	Het
Intu	T	C	3: 40,647,347 (GRCm39)	V740A	probably benign	Het
Itga2	C	T	13: 114,992,717 (GRCm39)	V838I	probably benign	Het
Kif9	A	G	9: 110,318,965 (GRCm39)	E143G	probably damaging	Het
Kmt2c	T	A	5: 25,614,205 (GRCm39)	I172F	probably benign	Het
Kmt2d	G	A	15: 98,754,043 (GRCm39)	R21W	probably damaging	Het
Mdh1b	A	T	1: 63,750,620 (GRCm39)	D449E	probably benign	Het
Meis1	T	C	11: 18,831,785 (GRCm39)	I418V	probably benign	Het
Nags	T	A	11: 102,037,395 (GRCm39)	M162K	probably damaging	Het
Nufip1	A	G	14: 76,348,413 (GRCm39)	D14G	probably benign	Het
Or2l13	T	A	16: 19,306,227 (GRCm39)	I213N	probably damaging	Het
Or2n1c	A	C	17: 38,519,208 (GRCm39)	E24A	possibly damaging	Het
Or7g28	T	G	9: 19,272,274 (GRCm39)	I126L	probably damaging	Het
Osmr	A	C	15: 6,850,560 (GRCm39)	V681G	probably damaging	Het
Paxip1	G	T	5: 27,971,282 (GRCm39)	Q356K	unknown	Het
Pcdhac1	T	A	18: 37,223,595 (GRCm39)	F136Y	probably damaging	Het
Pla2g6	A	G	15: 79,171,328 (GRCm39)	V699A	probably benign	Het
Plcb3	A	T	19: 6,943,578 (GRCm39)	V107E	probably damaging	Het
Plch1	T	A	3: 63,681,136 (GRCm39)	I164F	probably damaging	Het
Plpp3	A	T	4: 105,052,077 (GRCm39)	I73F	probably damaging	Het
Plscr5	G	A	9: 92,080,574 (GRCm39)	R20Q	probably benign	Het
Prdm10	G	A	9: 31,252,779 (GRCm39)	R504Q	probably damaging	Het
Prss58	T	C	6: 40,874,751 (GRCm39)	Y30C	probably damaging	Het
Psg19	T	A	7: 18,530,894 (GRCm39)	T87S	probably benign	Het
Ptpn22	T	G	3: 103,789,418 (GRCm39)	M294R	probably benign	Het
Rai1	T	A	11: 60,079,482 (GRCm39)	M1182K	probably benign	Het
Sez6	T	A	11: 77,867,388 (GRCm39)	V795D	possibly damaging	Het
Shcbp1	A	G	8: 4,789,214 (GRCm39)	V535A	possibly damaging	Het
Skint9	A	G	4: 112,246,447 (GRCm39)	Y222H	probably benign	Het
Slc13a3	T	A	2: 165,253,816 (GRCm39)	I446F	probably damaging	Het
Slc2a3	C	T	6: 122,714,196 (GRCm39)	R57H	probably damaging	Het
Slc44a4	A	G	17: 35,140,219 (GRCm39)	D208G	probably benign	Het
Spata31d1b	A	T	13: 59,863,838 (GRCm39)	N329Y	possibly damaging	Het
Strbp	C	T	2: 37,517,499 (GRCm39)	R192K	probably damaging	Het
Tctn3	A	T	19: 40,600,548 (GRCm39)	L14Q	probably damaging	Het
Tenm2	T	A	11: 36,834,989 (GRCm39)	D2V	probably damaging	Het
Tln2	T	G	9: 67,241,596 (GRCm39)	K1003T	probably benign	Het
Tmem63b	T	C	17: 45,971,800 (GRCm39)	E805G	probably damaging	Het
Trhr	A	T	15: 44,060,980 (GRCm39)	N167Y	probably damaging	Het
Trpc2	A	G	7: 101,744,390 (GRCm39)	R721G	probably benign	Het
Ttn	C	A	2: 76,701,267 (GRCm39)		probably benign	Het
Wdr91	A	G	6: 34,869,288 (GRCm39)	I412T	probably damaging	Het
Zcchc4	T	A	5: 52,953,952 (GRCm39)	S211T	probably benign	Het

Other mutations in Hdgfl2

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL01446:Hdgfl2	APN	17	56,404,281 (GRCm39)	missense	possibly damaging	0.94
IGL01486:Hdgfl2	APN	17	56,405,733 (GRCm39)	missense	possibly damaging	0.84
IGL02977:Hdgfl2	APN	17	56,406,319 (GRCm39)	missense	possibly damaging	0.71
IGL03196:Hdgfl2	APN	17	56,400,607 (GRCm39)	missense	probably benign	0.40
IGL03368:Hdgfl2	APN	17	56,386,746 (GRCm39)	utr 5 prime	probably benign
R0325:Hdgfl2	UTSW	17	56,406,181 (GRCm39)	missense	possibly damaging	0.95
R0635:Hdgfl2	UTSW	17	56,403,057 (GRCm39)	missense	probably damaging	0.99
R1914:Hdgfl2	UTSW	17	56,403,978 (GRCm39)	missense	probably damaging	1.00
R1927:Hdgfl2	UTSW	17	56,406,874 (GRCm39)	missense	possibly damaging	0.92
R2157:Hdgfl2	UTSW	17	56,405,691 (GRCm39)	missense	possibly damaging	0.46
R2337:Hdgfl2	UTSW	17	56,403,987 (GRCm39)	missense	possibly damaging	0.46
R4884:Hdgfl2	UTSW	17	56,403,265 (GRCm39)	missense	possibly damaging	0.91
R5510:Hdgfl2	UTSW	17	56,389,118 (GRCm39)	missense	possibly damaging	0.77
R6862:Hdgfl2	UTSW	17	56,406,211 (GRCm39)	missense	probably damaging	0.97
R7180:Hdgfl2	UTSW	17	56,404,532 (GRCm39)	splice site	probably null
R7389:Hdgfl2	UTSW	17	56,406,389 (GRCm39)	critical splice donor site	probably null
R7564:Hdgfl2	UTSW	17	56,406,860 (GRCm39)	missense	unknown
R7921:Hdgfl2	UTSW	17	56,400,724 (GRCm39)	critical splice donor site	probably null
R8168:Hdgfl2	UTSW	17	56,389,282 (GRCm39)	missense	probably damaging	0.98
R8348:Hdgfl2	UTSW	17	56,406,370 (GRCm39)	missense	possibly damaging	0.82
R8415:Hdgfl2	UTSW	17	56,400,712 (GRCm39)	missense	probably benign	0.19
R9070:Hdgfl2	UTSW	17	56,389,371 (GRCm39)	missense	possibly damaging	0.76
R9541:Hdgfl2	UTSW	17	56,405,976 (GRCm39)	missense	unknown
R9657:Hdgfl2	UTSW	17	56,405,978 (GRCm39)	missense	unknown
Z1176:Hdgfl2	UTSW	17	56,404,016 (GRCm39)	missense	probably null
Z1176:Hdgfl2	UTSW	17	56,386,825 (GRCm39)	missense	possibly damaging	0.79
Z1177:Hdgfl2	UTSW	17	56,406,343 (GRCm39)	missense	unknown

Predicted Primers

PCR Primer
(F):5'- ACAGATGTGGTAGCAACGCTG -3'
(R):5'- TTGCTGGGGACAAACATGGC -3'

Sequencing Primer
(F):5'- CAACGCTGAAGAAGGTATAGCATG -3'
(R):5'- GGGACAAACATGGCACTGTTCC -3'

Posted On

2016-06-06