Mutagenetix > Incidental Mutation

Incidental Mutation 'R0667:Klhdc3'

218563

Institutional Source

Beutler Lab

Gene Symbol

Klhdc3

Ensembl Gene

ENSMUSG00000063576

Gene Name

kelch domain containing 3

Synonyms

Peas, 1300011D16Rik

MMRRC Submission

038852-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.886) question?

Stock #

R0667 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

46985476-46991840 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to T at 46988151 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Phenylalanine to Isoleucine at position 205 (F205I)

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 benign
Transcript: ENSMUST00000071841
AA Change: F205I

PolyPhen 2 Score 0.072 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000071743
Gene: ENSMUSG00000063576
AA Change: F205I

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 benign
Transcript: ENSMUST00000165007
AA Change: F205I

PolyPhen 2 Score 0.072 (Sensitivity: 0.94; Specificity: 0.84)

SMART Domains

Protein: ENSMUSP00000128271
Gene: ENSMUSG00000063576
AA Change: F205I

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

0.1073

Coding Region Coverage

1x: 99.4%
3x: 98.8%
10x: 97.4%
20x: 94.8%

Validation Efficiency

98% (64/65)

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: 56 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
Abca5	G	T	11: 110,218,637 (GRCm39)	N76K	probably benign	Het
Adamts12	C	T	15: 11,215,710 (GRCm39)	R244C	probably damaging	Het
Atad2	A	G	15: 57,962,115 (GRCm39)	S1143P	probably benign	Het
Avl9	G	T	6: 56,713,468 (GRCm39)	R242L	probably benign	Het
Cand1	A	G	10: 119,052,425 (GRCm39)	S234P	probably benign	Het
Cd200	T	A	16: 45,215,220 (GRCm39)	I144L	probably benign	Het
Cep76	A	T	18: 67,767,848 (GRCm39)	L228Q	possibly damaging	Het
Col12a1	A	G	9: 79,535,744 (GRCm39)	L2584S	probably damaging	Het
Col6a3	A	C	1: 90,755,823 (GRCm39)	D155E	probably damaging	Het
Col6a4	G	A	9: 105,907,158 (GRCm39)		probably benign	Het
Dsg2	A	C	18: 20,706,556 (GRCm39)	D24A	possibly damaging	Het
Gm5901	G	A	7: 105,026,697 (GRCm39)	S155N	possibly damaging	Het
Hkdc1	T	C	10: 62,247,644 (GRCm39)		probably benign	Het
Kansl1	A	G	11: 104,234,364 (GRCm39)	V714A	probably benign	Het
Kcnh1	T	A	1: 192,188,346 (GRCm39)	S936T	probably benign	Het
Krt31	T	A	11: 99,938,951 (GRCm39)	H290L	probably benign	Het
Lama2	T	A	10: 27,220,406 (GRCm39)		probably null	Het
Mep1a	T	G	17: 43,789,081 (GRCm39)	D565A	probably benign	Het
Mgme1	T	A	2: 144,120,907 (GRCm39)		probably benign	Het
Mtf2	C	T	5: 108,252,369 (GRCm39)	T409I	probably damaging	Het
Mylk3	A	G	8: 86,081,794 (GRCm39)		probably null	Het
Myo1c	A	G	11: 75,559,338 (GRCm39)	E650G	probably damaging	Het
Nipbl	A	C	15: 8,390,488 (GRCm39)	D260E	possibly damaging	Het
Nufip2	T	A	11: 77,582,839 (GRCm39)	V251D	possibly damaging	Het
Or2n1e	C	A	17: 38,586,048 (GRCm39)	P129T	probably damaging	Het
Or4a2	T	C	2: 89,248,032 (GRCm39)	I242V	probably benign	Het
Or7g35	T	A	9: 19,496,743 (GRCm39)	N303K	probably benign	Het
Osm	G	T	11: 4,189,918 (GRCm39)	R234L	possibly damaging	Het
Pabpc1	G	A	15: 36,598,275 (GRCm39)	A515V	probably benign	Het
Piwil1	T	A	5: 128,818,542 (GRCm39)		probably null	Het
Pld1	A	G	3: 28,133,327 (GRCm39)		probably null	Het
Plekhg3	C	T	12: 76,623,372 (GRCm39)	R871C	probably damaging	Het
Ppfia2	A	T	10: 106,749,555 (GRCm39)	Y1147F	probably damaging	Het
Prmt3	A	G	7: 49,441,743 (GRCm39)	Y240C	probably damaging	Het
Prr36	G	T	8: 4,266,311 (GRCm39)		probably benign	Het
Ptprd	A	G	4: 75,875,583 (GRCm39)	I908T	probably damaging	Het
Sae1	A	T	7: 16,102,457 (GRCm39)	N172K	probably damaging	Het
Satb1	T	G	17: 52,089,889 (GRCm39)	Q319H	probably damaging	Het
Scart2	C	G	7: 139,841,450 (GRCm39)	S251R	possibly damaging	Het
Scn2a	A	T	2: 65,582,340 (GRCm39)	I1563F	possibly damaging	Het
Scn3a	C	A	2: 65,314,755 (GRCm39)	R1102L	probably null	Het
Serpinb9b	T	A	13: 33,216,909 (GRCm39)	L60*	probably null	Het
Setd1a	A	G	7: 127,385,765 (GRCm39)	D281G	probably damaging	Het
Slc8a1	C	A	17: 81,956,310 (GRCm39)	V243F	probably damaging	Het
Tgfbr3	A	T	5: 107,325,716 (GRCm39)	H115Q	probably benign	Het
Tiam1	C	A	16: 89,694,872 (GRCm39)	S195I	probably damaging	Het
Tjp2	A	G	19: 24,086,113 (GRCm39)	V803A	probably benign	Het
Ttc5	T	A	14: 51,003,415 (GRCm39)	Q423L	probably benign	Het
Tyk2	A	C	9: 21,020,167 (GRCm39)	V997G	probably damaging	Het
Uhrf1	T	C	17: 56,617,677 (GRCm39)	V133A	probably benign	Het
Vmn2r107	A	C	17: 20,575,916 (GRCm39)	Y82S	possibly damaging	Het
Vmn2r93	T	C	17: 18,546,503 (GRCm39)	F792L	probably damaging	Het
Vps13c	G	A	9: 67,858,855 (GRCm39)	W2768*	probably null	Het
Zfp456	A	T	13: 67,514,861 (GRCm39)	C282S	probably benign	Het
Zhx1	T	C	15: 57,916,561 (GRCm39)	N562D	possibly damaging	Het
Zmynd15	G	T	11: 70,355,944 (GRCm39)	G481C	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
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
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'- TCAGCCTTGCATTGTAGCCACC -3'
(R):5'- ATAGCTCAGCGAGTTTCTCCTGCC -3'

Sequencing Primer
(F):5'- TCTCCATTGTAGCCAACTGGAAG -3'
(R):5'- GAGTTTCTCCTGCCCGAGC -3'

Posted On

2014-08-18