Mutagenetix > Incidental Mutation

Incidental Mutation 'R5807:Klhdc3'

448615

Institutional Source

Beutler Lab

Gene Symbol

Klhdc3

Ensembl Gene

ENSMUSG00000063576

Gene Name

kelch domain containing 3

Synonyms

Peas, 1300011D16Rik

MMRRC Submission

043393-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.909) question?

Stock #

R5807 (G1)

Quality Score

225

Status

Validated

Chromosome

Chromosomal Location

46985476-46991840 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

T to C at 46988391 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Aspartic acid to Glycine at position 161 (D161G)

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: D161G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000071743
Gene: ENSMUSG00000063576
AA Change: D161G

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: D161G

PolyPhen 2 Score 0.978 (Sensitivity: 0.76; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000128271
Gene: ENSMUSG00000063576
AA Change: D161G

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

Meta Mutation Damage Score

0.9559

Coding Region Coverage

1x: 99.3%
3x: 98.7%
10x: 97.4%
20x: 95.7%

Validation Efficiency

98% (65/66)

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: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca12	A	G	1: 71,342,651 (GRCm39)	L943P	probably damaging	Het
Abcg5	C	A	17: 84,979,719 (GRCm39)	V214F	probably damaging	Het
Ang	T	A	14: 51,338,886 (GRCm39)		probably benign	Het
Arfgef3	A	G	10: 18,523,546 (GRCm39)		probably null	Het
Arhgef4	A	G	1: 34,846,696 (GRCm39)		probably benign	Het
Atp11b	T	C	3: 35,866,428 (GRCm39)	I409T	probably damaging	Het
Atp5f1b	G	A	10: 127,924,431 (GRCm39)		probably benign	Het
Atp9a	G	A	2: 168,495,454 (GRCm39)	A660V	probably damaging	Het
Avpr1a	A	G	10: 122,285,376 (GRCm39)	T223A	probably benign	Het
Bmp2k	T	C	5: 97,211,353 (GRCm39)	M507T	unknown	Het
Cep295	A	G	9: 15,243,828 (GRCm39)	S287P	probably damaging	Het
Chrna7	T	A	7: 62,798,349 (GRCm39)	D111V	probably damaging	Het
Clxn	A	T	16: 14,734,836 (GRCm39)	I69F	probably benign	Het
Cnr2	A	G	4: 135,644,747 (GRCm39)	D275G	probably benign	Het
Col28a1	T	A	6: 8,158,144 (GRCm39)	M305L	probably benign	Het
Cpb1	T	A	3: 20,317,906 (GRCm39)	D206V	probably damaging	Het
Cyp2c50	T	C	19: 40,101,944 (GRCm39)	L453S	probably damaging	Het
Ddx52	T	G	11: 83,840,508 (GRCm39)	S284A	probably benign	Het
Eif2ak4	G	T	2: 118,219,332 (GRCm39)	R48L	probably benign	Het
Esrrb	A	G	12: 86,561,175 (GRCm39)	E303G	possibly damaging	Het
Fbxo21	A	G	5: 118,114,933 (GRCm39)	E23G	probably benign	Het
Fcamr	T	C	1: 130,739,263 (GRCm39)	S188P	probably damaging	Het
Fer1l6	C	A	15: 58,462,399 (GRCm39)	S818*	probably null	Het
Fn1	T	C	1: 71,687,218 (GRCm39)	D213G	probably damaging	Het
Gcg	A	G	2: 62,306,069 (GRCm39)	I176T	possibly damaging	Het
Glis1	T	A	4: 107,425,279 (GRCm39)	S109T	probably benign	Het
Gm266	T	C	12: 111,452,173 (GRCm39)	D11G	probably benign	Het
Gm5070	C	A	3: 95,317,965 (GRCm39)		noncoding transcript	Het
Gm8444	T	C	15: 81,727,654 (GRCm39)		probably benign	Het
Golga4	A	G	9: 118,356,198 (GRCm39)	T117A	probably damaging	Het
Gpr132	G	A	12: 112,816,416 (GRCm39)	R137C	probably damaging	Het
Gvin-ps5	T	A	7: 105,929,430 (GRCm39)		noncoding transcript	Het
Herc2	T	A	7: 55,880,667 (GRCm39)	F4766L	probably damaging	Het
Inhbc	C	A	10: 127,193,411 (GRCm39)	E202*	probably null	Het
Kcnu1	C	T	8: 26,339,742 (GRCm39)	T20I	possibly damaging	Het
Krt84	T	A	15: 101,438,647 (GRCm39)	K280M	probably damaging	Het
Krtap9-5	T	A	11: 99,839,895 (GRCm39)	C199S	unknown	Het
Mrgprb3	A	G	7: 48,293,110 (GRCm39)	V147A	probably benign	Het
Ndufs6	A	T	13: 73,475,553 (GRCm39)	F48L	probably damaging	Het
Obscn	T	C	11: 58,970,476 (GRCm39)	S2586G	probably damaging	Het
Or10n1	A	G	9: 39,525,759 (GRCm39)	R299G	probably benign	Het
Or13c7b	C	A	4: 43,820,912 (GRCm39)	V150L	probably benign	Het
Or51a25	C	T	7: 102,373,409 (GRCm39)	R96H	possibly damaging	Het
Osbpl6	A	G	2: 76,414,857 (GRCm39)	D416G	probably damaging	Het
Pdilt	A	G	7: 119,099,766 (GRCm39)		probably benign	Het
Phf12	C	A	11: 77,913,252 (GRCm39)	D401E	probably benign	Het
Pla2r1	C	T	2: 60,259,065 (GRCm39)	V1108M	possibly damaging	Het
Prim2	A	G	1: 33,519,487 (GRCm39)		probably benign	Het
Ptpn6	T	C	6: 124,701,947 (GRCm39)	H406R	probably benign	Het
Qpctl	G	T	7: 18,877,132 (GRCm39)	H329N	probably damaging	Het
Ripk3	T	A	14: 56,022,755 (GRCm39)	N390Y	probably damaging	Het
Rnase1	A	G	14: 51,382,907 (GRCm39)	V149A	probably benign	Het
Rtn3	T	A	19: 7,434,192 (GRCm39)	D581V	probably damaging	Het
Slamf1	A	G	1: 171,602,630 (GRCm39)	Y119C	probably damaging	Het
Slc25a34	A	G	4: 141,350,973 (GRCm39)	M12T	probably benign	Het
Tmem38a	A	G	8: 73,333,944 (GRCm39)	Y141C	probably damaging	Het
Tnr	C	T	1: 159,714,500 (GRCm39)	T793I	possibly damaging	Het
Tns3	T	C	11: 8,443,211 (GRCm39)	D384G	probably damaging	Het
Vmn2r116	T	A	17: 23,606,281 (GRCm39)	Y398N	probably damaging	Het
Wee1	TCCCC	TCCC	7: 109,723,776 (GRCm39)		probably null	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
R4409:Klhdc3	UTSW	17	46,987,944 (GRCm39)	missense	probably damaging	1.00
R4799:Klhdc3	UTSW	17	46,988,226 (GRCm39)	missense	possibly damaging	0.82
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'- TGAGTGGAAGTCCCTCCAAC -3'
(R):5'- TATGAACAGCTGGTAAGTCTGG -3'

Sequencing Primer
(F):5'- TCCCTCCAACGTGCAGGATTG -3'
(R):5'- AGAAAAGAGAGAGAAATTTAGCATGG -3'

Posted On

2016-12-15