Incidental Mutation 'R6922:Lhfpl2'
ID 539692
Institutional Source Beutler Lab
Gene Symbol Lhfpl2
Ensembl Gene ENSMUSG00000045312
Gene Name lipoma HMGIC fusion partner-like 2
Synonyms vgim
MMRRC Submission 045041-MU
Accession Numbers
Essential gene? Probably non essential (E-score: 0.218) question?
Stock # R6922 (G1)
Quality Score 225.009
Status Not validated
Chromosome 13
Chromosomal Location 94194304-94331917 bp(+) (GRCm39)
Type of Mutation missense
DNA Base Change (assembly) G to T at 94311029 bp (GRCm39)
Zygosity Heterozygous
Amino Acid Change Alanine to Serine at position 100 (A100S)
Ref Sequence ENSEMBL: ENSMUSP00000152241 (fasta)
Gene Model predicted gene model for transcript(s): [ENSMUST00000054274] [ENSMUST00000118195] [ENSMUST00000120051] [ENSMUST00000121618] [ENSMUST00000156071] [ENSMUST00000221096] [ENSMUST00000223423]
AlphaFold Q8BGA2
Predicted Effect probably benign
Transcript: ENSMUST00000054274
AA Change: A100S

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000062239
Gene: ENSMUSG00000045312
AA Change: A100S

DomainStartEndE-ValueType
Pfam:L_HGMIC_fpl 9 198 2.3e-59 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000118195
AA Change: A100S

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000112655
Gene: ENSMUSG00000045312
AA Change: A100S

DomainStartEndE-ValueType
Pfam:L_HGMIC_fpl 9 198 2.4e-59 PFAM
Pfam:Claudin_2 16 197 3.9e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000120051
Predicted Effect probably benign
Transcript: ENSMUST00000121618
AA Change: A100S

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000113468
Gene: ENSMUSG00000045312
AA Change: A100S

DomainStartEndE-ValueType
Pfam:L_HGMIC_fpl 9 198 2.4e-59 PFAM
Pfam:Claudin_2 16 197 3.9e-12 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000156071
AA Change: A100S

PolyPhen 2 Score 0.123 (Sensitivity: 0.93; Specificity: 0.86)
SMART Domains Protein: ENSMUSP00000117113
Gene: ENSMUSG00000045312
AA Change: A100S

DomainStartEndE-ValueType
Pfam:L_HGMIC_fpl 9 139 2.3e-35 PFAM
Predicted Effect probably benign
Transcript: ENSMUST00000221096
Predicted Effect probably damaging
Transcript: ENSMUST00000223423
AA Change: A100S

PolyPhen 2 Score 1.000 (Sensitivity: 0.00; Specificity: 1.00)
Meta Mutation Damage Score 0.3859 question?
Coding Region Coverage
  • 1x: 100.0%
  • 3x: 99.9%
  • 10x: 99.3%
  • 20x: 97.7%
Validation Efficiency
MGI Phenotype FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene is a member of the lipoma HMGIC fusion partner (LHFP) gene family, which is a subset of the superfamily of tetraspan transmembrane protein encoding genes. Mutations in one LHFP-like gene result in deafness in humans and mice, and a second LHFP-like gene is fused to a high-mobility group gene in a translocation-associated lipoma. Alternatively spliced transcript variants have been found, but their biological validity has not been determined. [provided by RefSeq, Jul 2008]
PHENOTYPE: Females homozygous for a spontaneous point mutation have a completely closed vagina, soft swelling of the perineum and buildup of viscous fluid in the uteri. [provided by MGI curators]
Allele List at MGI
Other mutations in this stock
Total: 44 list
GeneRefVarChr/LocMutationPredicted EffectZygosity
Ago2 T C 15: 72,985,601 (GRCm39) I665V probably benign Het
Aoc1l3 T G 6: 48,964,508 (GRCm39) F172C probably damaging Het
Arhgap32 A T 9: 32,063,983 (GRCm39) M74L possibly damaging Het
Asb4 T C 6: 5,398,304 (GRCm39) C90R possibly damaging Het
B3galt4 T A 17: 34,169,821 (GRCm39) D139V probably damaging Het
Camta2 A C 11: 70,564,964 (GRCm39) I852S probably benign Het
Cd200l1 A T 16: 45,264,294 (GRCm39) M88K probably benign Het
Cox4i2 G T 2: 152,599,015 (GRCm39) E57D probably benign Het
Dip2b T C 15: 100,091,724 (GRCm39) I1055T probably benign Het
Eif1ad18 T A 12: 88,050,602 (GRCm39) W46R probably benign Het
Eif4g3 C T 4: 137,824,646 (GRCm39) P284S probably damaging Het
Ephb1 C A 9: 101,806,463 (GRCm39) probably null Het
Fbxw7 A T 3: 84,879,723 (GRCm39) probably null Het
Frem1 C A 4: 82,840,506 (GRCm39) D1789Y probably damaging Het
Gm29106 A T 1: 118,127,524 (GRCm39) R405S probably damaging Het
Greb1l G A 18: 10,547,482 (GRCm39) V1567M possibly damaging Het
Hapstr1 A G 16: 8,648,553 (GRCm39) probably null Het
Heatr1 C A 13: 12,449,956 (GRCm39) D1983E probably benign Het
Lrp5 A T 19: 3,655,301 (GRCm39) V1073D probably damaging Het
Naip6 G A 13: 100,438,706 (GRCm39) L364F possibly damaging Het
Nek9 A G 12: 85,350,311 (GRCm39) L921P probably damaging Het
Nim1k C T 13: 120,189,263 (GRCm39) E49K probably damaging Het
Nsun5 A C 5: 135,399,046 (GRCm39) N32T probably damaging Het
Nuggc T C 14: 65,855,092 (GRCm39) S325P probably damaging Het
Or2d36 A G 7: 106,747,290 (GRCm39) I256V probably damaging Het
Or5w12 T A 2: 87,501,797 (GRCm39) K305* probably null Het
Pcdhga7 A G 18: 37,848,710 (GRCm39) D239G probably damaging Het
Pld2 A G 11: 70,444,273 (GRCm39) D523G probably benign Het
Prokr1 C A 6: 87,565,455 (GRCm39) W130L probably damaging Het
Prpf8 A G 11: 75,381,562 (GRCm39) N266S probably damaging Het
Rdh10 T C 1: 16,176,255 (GRCm39) V5A probably benign Het
Rp1l1 T C 14: 64,267,834 (GRCm39) L1140P possibly damaging Het
Sacs A G 14: 61,448,874 (GRCm39) D3640G probably damaging Het
Smarca2 A G 19: 26,668,749 (GRCm39) E916G probably damaging Het
Steap3 A T 1: 120,171,624 (GRCm39) H160Q probably damaging Het
Tlk2 T C 11: 105,147,779 (GRCm39) probably null Het
Tmprss4 A G 9: 45,097,220 (GRCm39) V15A probably benign Het
Togaram2 T C 17: 72,014,129 (GRCm39) L559P probably damaging Het
Topbp1 T A 9: 103,213,045 (GRCm39) L990H probably damaging Het
Ttll7 A G 3: 146,615,369 (GRCm39) T278A possibly damaging Het
Ttn G A 2: 76,604,780 (GRCm39) L18385F probably damaging Het
Upf3a G T 8: 13,841,911 (GRCm39) A149S probably damaging Het
Vmn2r111 T C 17: 22,778,032 (GRCm39) N549S possibly damaging Het
Zfp316 A T 5: 143,239,280 (GRCm39) F913Y probably damaging Het
Other mutations in Lhfpl2
AlleleSourceChrCoordTypePredicted EffectPPH Score
IGL02106:Lhfpl2 APN 13 94,328,419 (GRCm39) missense probably benign 0.00
IGL02576:Lhfpl2 APN 13 94,310,734 (GRCm39) start codon destroyed probably null 1.00
R0278:Lhfpl2 UTSW 13 94,310,943 (GRCm39) missense probably benign 0.00
R0482:Lhfpl2 UTSW 13 94,311,118 (GRCm39) missense probably damaging 1.00
R1134:Lhfpl2 UTSW 13 94,310,760 (GRCm39) missense probably damaging 1.00
R2130:Lhfpl2 UTSW 13 94,328,557 (GRCm39) missense possibly damaging 0.91
R2302:Lhfpl2 UTSW 13 94,311,054 (GRCm39) missense probably benign 0.00
R2995:Lhfpl2 UTSW 13 94,310,966 (GRCm39) missense probably benign 0.04
R6613:Lhfpl2 UTSW 13 94,311,003 (GRCm39) missense probably damaging 1.00
R9347:Lhfpl2 UTSW 13 94,328,539 (GRCm39) missense probably damaging 0.99
R9480:Lhfpl2 UTSW 13 94,310,733 (GRCm39) start codon destroyed probably null 1.00
Predicted Primers PCR Primer
(F):5'- TGATCGGGAAAGCCAAGACC -3'
(R):5'- ACCAGAGGAACGGGATCTTG -3'

Sequencing Primer
(F):5'- GGAAAGCCAAGACCCGCAG -3'
(R):5'- TCTTCAACAGATGCAAGCAGTAAGTG -3'
Posted On 2018-11-06