Lct MGI Mouse Gene Detail - MGI:104576

Symbol

Lct
Name

lactase
Synonyms

LOC226413, LPH, Lphl

Feature Type

protein coding gene
IDs

MGI:104576
NCBI Gene: 226413
Alliance

gene page
Transcription Start Sites

9 TSS

Sequence Map

Chr1:128212493-128256055 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 55.80 cM
Mapping Data

7 experiments

SNPs within 2kb

1204 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_104576	protein coding gene	Chr1:128212493-128256055 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0016428	protein coding gene	Chr1:131523029-131569118 (-)
A/J	MGP_AJ_G0016411	protein coding gene	Chr1:126618262-126661207 (-)
AKR/J	MGP_AKRJ_G0016376	protein coding gene	Chr1:130366999-130411857 (-)
BALB/cJ	MGP_BALBcJ_G0016371	protein coding gene	Chr1:126993969-127038090 (-)
C3H/HeJ	MGP_C3HHeJ_G0016197	protein coding gene	Chr1:130531815-130575026 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0016832	protein coding gene	Chr1:136464726-136516937 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014545	protein coding gene	Chr1:119975315-120019352 (-)
CAST/EiJ	MGP_CASTEiJ_G0015778	protein coding gene	Chr1:129507725-129560014 (-)
CBA/J	MGP_CBAJ_G0016170	protein coding gene	Chr1:141059356-141121753 (-)
DBA/2J	MGP_DBA2J_G0016276	protein coding gene	Chr1:125655448-125698556 (-)
FVB/NJ	MGP_FVBNJ_G0016275	protein coding gene	Chr1:124373372-124415917 (-)
LP/J	MGP_LPJ_G0016347	protein coding gene	Chr1:132870895-132916822 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016300	protein coding gene	Chr1:146916433-146965959 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0016868	protein coding gene	Chr1:130138276-130191149 (-)
PWK/PhJ	MGP_PWKPhJ_G0015564	protein coding gene	Chr1:124626025-124675915 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0015352	protein coding gene	Chr1:129097169-129141758 (-)
WSB/EiJ	MGP_WSBEiJ_G0015840	protein coding gene	Chr1:130097537-130149098 (-)

Human Ortholog

LCT, lactase

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LCT, lactase
Synonyms

LAC, LPH, LPH1
Links

HGNC:6530

NCBI Gene ID: 3938

neXtProt AC: NX_P09848

UniProt: P09848
Chr Location

2q21.3; chr2:135787850-135837184 (-) GRCh38

MGI Vertebrate Homology

Lct stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: LCT
Gene Tree

Lct

Diseases

1 with human LCT associations

				Human Disease	Mouse Models
				congenital lactase deficiency IDs congenital lactase deficiency DOID:0111646 ICD10CM:E73.0 MESH:C562600 OMIM:223000 ORDO:53690 UMLS_CUI:C0268179

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

2 phenotypes from 1 allele in 1 genetic background
10 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

6
Chemically induced (other)

2
Radiation induced

1
Targeted

3
Genomic Mutations

3 involving Lct
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

94 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

26
GO References

3

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

708
Tissues

1
cDNA Data

18
Literature Summary

11

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lct.2, LOC101732850

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All Sequences

32
RefSeq

2
UniProt

3
CCDS

CCDS35698.1

Ensembl

ENSMUSG00000026354 (Evidence)
NCBI Gene

226413

			Length	Strain/Species	Flank
genomic	226413	NCBI Gene Model \| MGI Sequence Detail	43563	C57BL/6J	± kb
transcript	NM_001081078	RefSeq \| MGI Sequence Detail	6174	ZRU/MplStud
polypeptide	NP_001074547	RefSeq \| MGI Sequence Detail	1931	ZRU/MplStud

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UniProt

3 Sequences
InterPro Domains

IPR001360 Glycoside hydrolase family 1

IPR018120 Glycoside hydrolase family 1, active site

IPR017853 Glycoside hydrolase superfamily

IPR033132 Glycosyl hydrolases family 1, N-terminal conserved site

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All nucleic 21

cDNA 19

Primer pair 2

Microarray probesets 3

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MGD-MRK-26010, MGI:1261815, MGI:2684946

Summaries

All 51

Developmental Gene Expression 11

Gene Ontology 3

Phenotypes 10
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Lct:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr13448	Chr1:128256048-128256063 (-)	-1 bp
Tssr13447	Chr1:128255486-128255492 (-)	566 bp
Tssr13446	Chr1:128252234-128252239 (-)	3,818 bp
Tssr13445	Chr1:128252060-128252064 (-)	3,993 bp
Tssr13444	Chr1:128246957-128246975 (-)	9,089 bp
Tssr13443	Chr1:128246835-128246851 (-)	9,212 bp
Tssr13442	Chr1:128227690-128227724 (-)	28,348 bp
Tssr13441	Chr1:128227326-128227371 (-)	28,706 bp
Tssr13440	Chr1:128227242-128227261 (-)	28,803 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/10/2024 MGI 6.24