Mutagenetix > Incidental Mutation

Incidental Mutation 'R4409:Klhdc3'

327835

Institutional Source

Beutler Lab

Gene Symbol

Klhdc3

Ensembl Gene

ENSMUSG00000063576

Gene Name

kelch domain containing 3

Synonyms

Peas, 1300011D16Rik

MMRRC Submission

041691-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.886) question?

Stock #

R4409 (G1)

Quality Score

225

Status

Not validated

Chromosome

Chromosomal Location

46985476-46991840 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

C to T at 46987944 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Glycine to Glutamic Acid at position 249 (G249E)

Ref Sequence

ENSEMBL: ENSMUSP00000128271 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000002845] [ENSMUST00000024766] [ENSMUST00000071841] [ENSMUST00000165007]

AlphaFold

no structure available at present

Predicted Effect

probably benign
Transcript: ENSMUST00000002845

SMART Domains

Protein: ENSMUSP00000002845
Gene: ENSMUSG00000002768

Domain	Start	End	E-Value	Type
Pfam:MEA1	1	174	1.6e-121	PFAM

Predicted Effect

probably benign
Transcript: ENSMUST00000024766

SMART Domains

Protein: ENSMUSP00000024766
Gene: ENSMUSG00000023971

Domain	Start	End	E-Value	Type
Pfam:DUF947	55	219	7.6e-53	PFAM

Predicted Effect

probably damaging
Transcript: ENSMUST00000071841
AA Change: G249E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000071743
Gene: ENSMUSG00000063576
AA Change: G249E

Domain	Start	End	E-Value	Type
Pfam:Kelch_1	13	63	1.6e-8	PFAM
Pfam:Kelch_2	13	63	2.2e-9	PFAM
Pfam:Kelch_4	13	65	3.8e-8	PFAM
Pfam:Kelch_6	13	67	9.6e-11	PFAM
Pfam:Kelch_5	73	113	3.1e-8	PFAM
Pfam:Kelch_1	76	117	1.9e-7	PFAM
Pfam:Kelch_6	76	121	1.7e-9	PFAM
Pfam:Kelch_2	77	121	2.1e-8	PFAM
Pfam:Kelch_4	77	125	4.6e-11	PFAM
Pfam:Kelch_3	86	136	1.3e-12	PFAM
Pfam:Kelch_1	127	172	1.5e-10	PFAM
Pfam:Kelch_6	127	173	2e-10	PFAM
Pfam:Kelch_2	127	174	4.7e-14	PFAM
Pfam:Kelch_4	127	177	1.3e-10	PFAM
Pfam:Kelch_2	179	231	2.4e-8	PFAM
Pfam:Kelch_1	180	233	5.8e-9	PFAM
Pfam:Kelch_3	189	247	7.3e-8	PFAM
Pfam:Kelch_5	235	276	1.2e-11	PFAM
Pfam:Kelch_1	238	284	2.7e-8	PFAM
Pfam:Kelch_6	238	293	2.4e-12	PFAM
Pfam:Kelch_3	248	299	4.2e-10	PFAM
low complexity region	322	333	N/A	INTRINSIC

Predicted Effect

probably damaging
Transcript: ENSMUST00000165007
AA Change: G249E

PolyPhen 2 Score 0.998 (Sensitivity: 0.27; Specificity: 0.99)

SMART Domains

Protein: ENSMUSP00000128271
Gene: ENSMUSG00000063576
AA Change: G249E

Domain	Start	End	E-Value	Type
Pfam:Kelch_1	13	63	9.9e-10	PFAM
Pfam:Kelch_2	13	63	2.2e-9	PFAM
Pfam:Kelch_6	13	66	7.5e-11	PFAM
Pfam:Kelch_4	13	71	1.4e-8	PFAM
Pfam:Kelch_5	73	113	3e-8	PFAM
Pfam:Kelch_1	76	118	2.6e-8	PFAM
Pfam:Kelch_6	76	121	1.1e-10	PFAM
Pfam:Kelch_4	76	126	2e-11	PFAM
Pfam:Kelch_2	77	121	2.1e-8	PFAM
Pfam:Kelch_3	86	136	7.7e-12	PFAM
Pfam:Kelch_1	127	170	1.2e-8	PFAM
Pfam:Kelch_2	127	174	4.7e-14	PFAM
Pfam:Kelch_4	127	177	1.7e-7	PFAM
Pfam:Kelch_2	179	231	2.4e-8	PFAM
Pfam:Kelch_6	179	239	2.5e-9	PFAM
Pfam:Kelch_1	180	232	3.4e-8	PFAM
Pfam:Kelch_3	189	247	5.7e-8	PFAM
Pfam:Kelch_5	235	276	4.3e-10	PFAM
Pfam:Kelch_1	238	285	9.3e-10	PFAM
Pfam:Kelch_4	238	291	9.9e-8	PFAM
Pfam:Kelch_6	238	293	2.5e-12	PFAM
Pfam:Kelch_3	248	299	1.1e-9	PFAM
low complexity region	322	333	N/A	INTRINSIC

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000181301

Coding Region Coverage

1x: 99.2%
3x: 98.6%
10x: 97.3%
20x: 95.4%

Validation Efficiency

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] The protein encoded by this gene contains six repeated kelch motifs that are structurally similar to recombination activating gene 2, a protein involved in the activation of the V(D)J recombination. In mouse, this gene is found to be expressed specifically in testis. Its expression in pachytene spermatocytes is localized to cytoplasma and meiotic chromatin, suggesting that this gene may be involved in meiotic recombination. [provided by RefSeq, Jun 2012]

Allele List at MGI

Other mutations in this stock

Total: 61 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
AAdacl4fm3	A	T	4: 144,447,872 (GRCm39)	S35T	possibly damaging	Het
Abcb5	A	C	12: 118,836,657 (GRCm39)	L1085V	probably damaging	Het
Adgrf5	T	C	17: 43,752,738 (GRCm39)	V560A	probably damaging	Het
Ambp	C	A	4: 63,070,884 (GRCm39)	S65I	probably damaging	Het
Ash1l	A	G	3: 88,914,506 (GRCm39)	D1712G	probably damaging	Het
Capn7	T	C	14: 31,077,296 (GRCm39)	L338P	probably damaging	Het
Car2	T	A	3: 14,960,162 (GRCm39)	S105T	probably damaging	Het
Casr	A	G	16: 36,320,703 (GRCm39)	C482R	probably benign	Het
Ccdc18	C	T	5: 108,368,708 (GRCm39)	Q1277*	probably null	Het
Clca3a1	A	G	3: 144,711,788 (GRCm39)	F736L	probably damaging	Het
Col6a1	T	C	10: 76,557,334 (GRCm39)	H206R	probably benign	Het
Crybg1	C	T	10: 43,874,754 (GRCm39)	A785T	possibly damaging	Het
Cyp2c68	T	A	19: 39,727,896 (GRCm39)	E85D	probably damaging	Het
Dnah9	T	C	11: 65,976,303 (GRCm39)	S1249G	possibly damaging	Het
E2f1	C	G	2: 154,405,942 (GRCm39)	G144R	probably damaging	Het
Fbxw24	A	T	9: 109,437,256 (GRCm39)	D210E	probably damaging	Het
Fcgr1	T	C	3: 96,191,893 (GRCm39)	Y305C	probably benign	Het
Gm10226	G	T	17: 21,910,876 (GRCm39)	C37F	possibly damaging	Het
Greb1l	A	G	18: 10,503,182 (GRCm39)	Y411C	possibly damaging	Het
Grin1	T	C	2: 25,200,451 (GRCm39)	N224D	possibly damaging	Het
H2-T5	T	A	17: 36,476,742 (GRCm39)	H244L	possibly damaging	Het
Ighmbp2	C	T	19: 3,321,536 (GRCm39)	V408I	probably benign	Het
Il1rap	G	A	16: 26,531,015 (GRCm39)		probably null	Het
Iqcg	A	G	16: 32,865,888 (GRCm39)		probably null	Het
Lct	T	C	1: 128,231,963 (GRCm39)	M629V	probably damaging	Het
Macrod2	T	G	2: 140,260,777 (GRCm39)	H68Q	possibly damaging	Het
Morn4	T	C	19: 42,066,986 (GRCm39)	T2A	possibly damaging	Het
Msc	G	C	1: 14,825,902 (GRCm39)	P24R	probably damaging	Het
Msh5	T	C	17: 35,258,226 (GRCm39)	D300G	probably damaging	Het
Myo10	A	G	15: 25,807,955 (GRCm39)	Y1859C	probably damaging	Het
Nacc1	A	G	8: 85,399,673 (GRCm39)	*515Q	probably null	Het
Or1ad6	T	A	11: 50,860,223 (GRCm39)	I126N	probably damaging	Het
Or4n5	T	A	14: 50,133,230 (GRCm39)	T10S	probably benign	Het
Or5g29	T	C	2: 85,421,274 (GRCm39)	L130S	probably damaging	Het
Oxgr1	C	T	14: 120,259,572 (GRCm39)	V212M	possibly damaging	Het
P3h2	G	C	16: 25,924,040 (GRCm39)	R132G	possibly damaging	Het
Pcdha9	T	A	18: 37,132,198 (GRCm39)	H422Q	probably benign	Het
Pcdhga12	A	G	18: 37,901,138 (GRCm39)	T657A	probably damaging	Het
Pcx	A	G	19: 4,660,031 (GRCm39)	K442R	possibly damaging	Het
Pkd2	T	C	5: 104,614,750 (GRCm39)		silent	Het
Plg	T	G	17: 12,609,150 (GRCm39)	C152G	probably damaging	Het
Plk4	A	G	3: 40,760,984 (GRCm39)	E438G	probably damaging	Het
Ryr3	A	G	2: 112,560,653 (GRCm39)	L3016P	probably damaging	Het
Sdccag8	T	G	1: 176,695,932 (GRCm39)		probably null	Het
Slc24a1	A	T	9: 64,855,506 (GRCm39)	M467K	probably benign	Het
Sorl1	T	G	9: 41,946,744 (GRCm39)	I856L	probably damaging	Het
Spag7	T	C	11: 70,555,688 (GRCm39)	D83G	probably damaging	Het
Tmem59l	A	G	8: 70,939,951 (GRCm39)	L6S	unknown	Het
Tmprss11b	T	C	5: 86,812,137 (GRCm39)	N170S	probably benign	Het
Tnfrsf1b	G	A	4: 144,950,855 (GRCm39)	Q253*	probably null	Het
Trim12a	G	A	7: 103,956,201 (GRCm39)	A113V	probably benign	Het
Ttn	A	G	2: 76,727,987 (GRCm39)		probably benign	Het
Vmn1r213	A	C	13: 23,195,593 (GRCm39)		probably benign	Het
Vmn1r54	C	A	6: 90,246,864 (GRCm39)	Y259*	probably null	Het
Vmn1r55	A	G	7: 5,150,075 (GRCm39)	V116A	probably benign	Het
Vmn2r120	T	C	17: 57,816,477 (GRCm39)	N626S	probably damaging	Het
Vmn2r58	A	G	7: 41,522,051 (GRCm39)	F15S	possibly damaging	Het
Vmn2r73	A	T	7: 85,520,768 (GRCm39)	V400E	probably damaging	Het
Zbtb39	A	G	10: 127,578,696 (GRCm39)	I423M	possibly damaging	Het
Zfp352	A	G	4: 90,113,401 (GRCm39)	N514D	probably benign	Het
Zfp451	A	T	1: 33,816,494 (GRCm39)	H485Q	probably damaging	Het

Other mutations in Klhdc3

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL02491:Klhdc3	APN	17	46,988,226 (GRCm39)	missense	possibly damaging	0.82
pinto	UTSW	17	46,988,972 (GRCm39)	missense	probably benign	0.36
shetland	UTSW	17	46,989,218 (GRCm39)	missense	possibly damaging	0.63
R0667:Klhdc3	UTSW	17	46,988,151 (GRCm39)	missense	probably benign	0.07
R0960:Klhdc3	UTSW	17	46,987,444 (GRCm39)	missense	possibly damaging	0.89
R1254:Klhdc3	UTSW	17	46,988,993 (GRCm39)	missense	probably benign
R1263:Klhdc3	UTSW	17	46,987,892 (GRCm39)	missense	probably benign	0.00
R1954:Klhdc3	UTSW	17	46,988,901 (GRCm39)	missense	probably damaging	1.00
R2093:Klhdc3	UTSW	17	46,988,879 (GRCm39)	missense	probably benign	0.00
R3808:Klhdc3	UTSW	17	46,988,858 (GRCm39)	missense	possibly damaging	0.89
R3809:Klhdc3	UTSW	17	46,988,858 (GRCm39)	missense	possibly damaging	0.89
R4799:Klhdc3	UTSW	17	46,988,226 (GRCm39)	missense	possibly damaging	0.82
R5807:Klhdc3	UTSW	17	46,988,391 (GRCm39)	missense	probably damaging	0.98
R5958:Klhdc3	UTSW	17	46,986,028 (GRCm39)	missense	probably benign	0.12
R6152:Klhdc3	UTSW	17	46,988,633 (GRCm39)	missense	probably damaging	1.00
R6295:Klhdc3	UTSW	17	46,988,972 (GRCm39)	missense	probably benign	0.36
R6521:Klhdc3	UTSW	17	46,988,687 (GRCm39)	missense	probably benign	0.20
R6851:Klhdc3	UTSW	17	46,989,218 (GRCm39)	missense	possibly damaging	0.63
R7524:Klhdc3	UTSW	17	46,989,340 (GRCm39)	missense	probably damaging	0.99
R8790:Klhdc3	UTSW	17	46,991,626 (GRCm39)	critical splice donor site	probably benign
Z1177:Klhdc3	UTSW	17	46,987,677 (GRCm39)	missense	probably damaging	0.99

Predicted Primers

PCR Primer
(F):5'- GTTCACTACCTGGCCAACCTAG -3'
(R):5'- GGGCCATTTCATTCCAACAATG -3'

Sequencing Primer
(F):5'- TGGCCAACCTAGACACCTAC -3'
(R):5'- CCAACAATGAGATCTACTGTAATCG -3'

Posted On

2015-07-07