MCID: LCT013
MIFTS: 24

Lactase Deficiency, Congenital

Categories: Genetic diseases, Rare diseases, Metabolic diseases, Gastrointestinal diseases

Aliases & Classifications for Lactase Deficiency, Congenital

MalaCards integrated aliases for Lactase Deficiency, Congenital:

Name: Lactase Deficiency, Congenital 57 13 55 40 73
Congenital Lactase Deficiency 53 59 75 37 29 6
Disaccharide Intolerance Ii 57 75
Alactasia, Congenital 57
Hereditary Alactasia 75
Colacd 75

Characteristics:

Orphanet epidemiological data:

59
congenital lactase deficiency
Inheritance: Autosomal recessive;

OMIM:

57
Inheritance:
autosomal recessive

Miscellaneous:
increased frequency in finland (incidence 1:60,000 finnish newborns)
onset day of life 1-10 in infants fed lactose-containing milk


HPO:

32
lactase deficiency, congenital:
Inheritance autosomal recessive inheritance


Classifications:



External Ids:

OMIM 57 223000
Orphanet 59 ORPHA53690
UMLS via Orphanet 74 C0268179
ICD10 via Orphanet 34 E73.0
MedGen 42 C0268179
KEGG 37 H00116
ICD10 33 E73.0
UMLS 73 C0268179

Summaries for Lactase Deficiency, Congenital

UniProtKB/Swiss-Prot : 75 Congenital lactase deficiency: Autosomal recessive, rare and severe gastrointestinal disorder. It is characterized by watery diarrhea in infants fed with breast milk or other lactose-containing formulas. An almost total lack of LCT activity is found in jejunal biopsy material of patients with congenital lactase deficiency. Opposite to congenital lactase deficiency, also known as lactose intolerance, is the most common enzyme deficiency worldwide. It is caused by developmental down- regulation of lactase activity during childhood or early adulthood. The decline of lactase activity is a normal physiological phenomenon; however, the majority of Northern Europeans have the ability to maintain lactase activity and digest lactose throughout life (lactase persistence). The down-regulation of lactase activity operates at the transcriptional level and it is associated with a noncoding variation in the MCM6 gene, located in the upstream vicinity of LCT.

MalaCards based summary : Lactase Deficiency, Congenital, also known as congenital lactase deficiency, is related to nephrocalcinosis. An important gene associated with Lactase Deficiency, Congenital is LCT (Lactase), and among its related pathways/superpathways is Galactose metabolism. Affiliated tissues include small intestine, and related phenotypes are dehydration and diarrhea

OMIM : 57 Congenital lactase deficiency is a severe gastrointestinal disorder characterized by watery diarrhea in infants fed with breast milk or other lactose-containing formulas. (223000)

Related Diseases for Lactase Deficiency, Congenital

Diseases related to Lactase Deficiency, Congenital via text searches within MalaCards or GeneCards Suite gene sharing:

# Related Disease Score Top Affiliating Genes
1 nephrocalcinosis 9.8

Symptoms & Phenotypes for Lactase Deficiency, Congenital

Symptoms via clinical synopsis from OMIM:

57
Abdomen Gastrointestinal:
neonatal diarrhea

Laboratory Abnormalities:
decreased-absent intestinal mucosa lactase activity
normal maltase, isomaltase, and sucrase activity

Metabolic Features:
dehydration
metabolic acidosis


Clinical features from OMIM:

223000

Human phenotypes related to Lactase Deficiency, Congenital:

32
# Description HPO Frequency HPO Source Accession
1 dehydration 32 HP:0001944
2 diarrhea 32 HP:0002014
3 metabolic acidosis 32 HP:0001942
4 lactose intolerance 32 HP:0004789
5 decreased small intestinal mucosa lactase activity 32 HP:0025130

Drugs & Therapeutics for Lactase Deficiency, Congenital

Search Clinical Trials , NIH Clinical Center for Lactase Deficiency, Congenital

Genetic Tests for Lactase Deficiency, Congenital

Genetic tests related to Lactase Deficiency, Congenital:

# Genetic test Affiliating Genes
1 Congenital Lactase Deficiency 29 LCT

Anatomical Context for Lactase Deficiency, Congenital

MalaCards organs/tissues related to Lactase Deficiency, Congenital:

41
Small Intestine

Publications for Lactase Deficiency, Congenital

Articles related to Lactase Deficiency, Congenital:

(show all 12)
# Title Authors Year
1
Two novel mutations in the lactase gene in a Japanese infant with congenital lactase deficiency. ( 22688420 )
2012
2
[Congenital lactase deficiency--a more common disease than previously thought?]. ( 19432082 )
2009
3
Impaired trafficking and subcellular localization of a mutant lactase associated with congenital lactase deficiency. ( 19208354 )
2009
4
Four novel mutations in the lactase gene (LCT) underlying congenital lactase deficiency (CLD). ( 19161632 )
2009
5
Molecular differentiation of congenital lactase deficiency from adult-type hypolactasia. ( 17345962 )
2007
6
Mutations in the translated region of the lactase gene (LCT) underlie congenital lactase deficiency. ( 16400612 )
2006
7
Assignment of the locus for congenital lactase deficiency to 2q21, in the vicinity of but separate from the lactase-phlorizin hydrolase gene. ( 9758622 )
1998
8
Hypercalcemia and nephrocalcinosis in patients with congenital lactase deficiency. ( 8523189 )
1995
9
Congenital lactase deficiency. A clinical study on 16 patients. ( 6847226 )
1983
10
Use of lactose-hydrolyzed human milk in congenital lactase deficiency. ( 7119963 )
1982
11
Intestinal beta-galactosidases in adult low lactase activity and in congenital lactase deficiency. ( 4852526 )
1974
12
Congenital lactase deficiency. ( 5946649 )
1966

Variations for Lactase Deficiency, Congenital

UniProtKB/Swiss-Prot genetic disease variations for Lactase Deficiency, Congenital:

75
# Symbol AA change Variation ID SNP ID
1 LCT p.Gln268His VAR_026706 rs121908937
2 LCT p.Gly1363Ser VAR_026708 rs386833833

ClinVar genetic disease variations for Lactase Deficiency, Congenital:

6
(show top 50) (show all 141)
# Gene Variation Type Significance SNP ID Assembly Location
1 LCT NM_002299.3(LCT): c.4170T> A (p.Tyr1390Ter) single nucleotide variant Pathogenic rs121908936 GRCh37 Chromosome 2, 136564701: 136564701
2 LCT NM_002299.3(LCT): c.4170T> A (p.Tyr1390Ter) single nucleotide variant Pathogenic rs121908936 GRCh38 Chromosome 2, 135807131: 135807131
3 LCT LCT, 4-BP DEL, NT4998 deletion Pathogenic
4 LCT NM_002299.3(LCT): c.804G> C (p.Gln268His) single nucleotide variant Pathogenic rs121908937 GRCh37 Chromosome 2, 136587163: 136587163
5 LCT NM_002299.3(LCT): c.804G> C (p.Gln268His) single nucleotide variant Pathogenic rs121908937 GRCh38 Chromosome 2, 135829593: 135829593
6 LCT NM_002299.3(LCT): c.1692_1696delAGTGG (p.Val565Leufs) deletion Likely pathogenic rs386833832 GRCh37 Chromosome 2, 136574922: 136574926
7 LCT NM_002299.3(LCT): c.1692_1696delAGTGG (p.Val565Leufs) deletion Likely pathogenic rs386833832 GRCh38 Chromosome 2, 135817352: 135817356
8 LCT NM_002299.3(LCT): c.4087G> A (p.Gly1363Ser) single nucleotide variant Likely pathogenic rs386833833 GRCh37 Chromosome 2, 136564784: 136564784
9 LCT NM_002299.3(LCT): c.4087G> A (p.Gly1363Ser) single nucleotide variant Likely pathogenic rs386833833 GRCh38 Chromosome 2, 135807214: 135807214
10 LCT NM_002299.3(LCT): c.4419C> G (p.Tyr1473Ter) single nucleotide variant Likely pathogenic rs386833834 GRCh37 Chromosome 2, 136562382: 136562382
11 LCT NM_002299.3(LCT): c.4419C> G (p.Tyr1473Ter) single nucleotide variant Likely pathogenic rs386833834 GRCh38 Chromosome 2, 135804812: 135804812
12 LCT NM_002299.3(LCT): c.4834G> T (p.Glu1612Ter) single nucleotide variant Likely pathogenic rs386833835 GRCh37 Chromosome 2, 136558209: 136558209
13 LCT NM_002299.3(LCT): c.4834G> T (p.Glu1612Ter) single nucleotide variant Likely pathogenic rs386833835 GRCh38 Chromosome 2, 135800639: 135800639
14 LCT NM_002299.3(LCT): c.4998_5001delTGAG (p.Ser1666Argfs) deletion Likely pathogenic rs386833836 GRCh37 Chromosome 2, 136552321: 136552324
15 LCT NM_002299.3(LCT): c.4998_5001delTGAG (p.Ser1666Argfs) deletion Likely pathogenic rs386833836 GRCh38 Chromosome 2, 135794751: 135794754
16 LCT NM_002299.3(LCT): c.5387delA (p.Asp1796Alafs) deletion Likely pathogenic rs386833837 GRCh37 Chromosome 2, 136547317: 136547317
17 LCT NM_002299.3(LCT): c.5387delA (p.Asp1796Alafs) deletion Likely pathogenic rs386833837 GRCh38 Chromosome 2, 135789747: 135789747
18 LCT NM_002299.3(LCT): c.653_654delCT (p.Ser218Cysfs) deletion Likely pathogenic rs386833838 GRCh37 Chromosome 2, 136590747: 136590748
19 LCT NM_002299.3(LCT): c.653_654delCT (p.Ser218Cysfs) deletion Likely pathogenic rs386833838 GRCh38 Chromosome 2, 135833177: 135833178
20 LCT NM_002299.3(LCT): c.*444_*445delGT deletion Likely benign rs140433552 GRCh38 Chromosome 2, 135787879: 135787880
21 LCT NM_002299.3(LCT): c.*444_*445delGT deletion Likely benign rs140433552 GRCh37 Chromosome 2, 136545449: 136545450
22 LCT NM_002299.3(LCT): c.*50G> C single nucleotide variant Benign rs1042712 GRCh38 Chromosome 2, 135788274: 135788274
23 LCT NM_002299.3(LCT): c.*50G> C single nucleotide variant Benign rs1042712 GRCh37 Chromosome 2, 136545844: 136545844
24 LCT NM_002299.3(LCT): c.5529C> T (p.Pro1843=) single nucleotide variant Uncertain significance rs761696901 GRCh38 Chromosome 2, 135789605: 135789605
25 LCT NM_002299.3(LCT): c.5529C> T (p.Pro1843=) single nucleotide variant Uncertain significance rs761696901 GRCh37 Chromosome 2, 136547175: 136547175
26 LCT NM_002299.3(LCT): c.4922T> C (p.Val1641Ala) single nucleotide variant Uncertain significance rs557029000 GRCh38 Chromosome 2, 135798083: 135798083
27 LCT NM_002299.3(LCT): c.4922T> C (p.Val1641Ala) single nucleotide variant Uncertain significance rs557029000 GRCh37 Chromosome 2, 136555653: 136555653
28 LCT NM_002299.3(LCT): c.4777G> A (p.Val1593Met) single nucleotide variant Likely benign rs35891837 GRCh38 Chromosome 2, 135800696: 135800696
29 LCT NM_002299.3(LCT): c.4777G> A (p.Val1593Met) single nucleotide variant Likely benign rs35891837 GRCh37 Chromosome 2, 136558266: 136558266
30 LCT NM_002299.3(LCT): c.4695C> T (p.Tyr1565=) single nucleotide variant Uncertain significance rs886054862 GRCh38 Chromosome 2, 135800778: 135800778
31 LCT NM_002299.3(LCT): c.4695C> T (p.Tyr1565=) single nucleotide variant Uncertain significance rs886054862 GRCh37 Chromosome 2, 136558348: 136558348
32 LCT NM_002299.3(LCT): c.4606C> T (p.Leu1536=) single nucleotide variant Benign rs2304371 GRCh38 Chromosome 2, 135803987: 135803987
33 LCT NM_002299.3(LCT): c.4606C> T (p.Leu1536=) single nucleotide variant Benign rs2304371 GRCh37 Chromosome 2, 136561557: 136561557
34 LCT NM_002299.3(LCT): c.4347T> C (p.Phe1449=) single nucleotide variant Uncertain significance rs17699796 GRCh38 Chromosome 2, 135804884: 135804884
35 LCT NM_002299.3(LCT): c.4347T> C (p.Phe1449=) single nucleotide variant Uncertain significance rs17699796 GRCh37 Chromosome 2, 136562454: 136562454
36 LCT NM_002299.3(LCT): c.4173+6_4173+8delGAG deletion Uncertain significance rs375300532 GRCh38 Chromosome 2, 135807120: 135807122
37 LCT NM_002299.3(LCT): c.4173+6_4173+8delGAG deletion Uncertain significance rs375300532 GRCh37 Chromosome 2, 136564690: 136564692
38 LCT NM_002299.3(LCT): c.3286G> A (p.Ala1096Thr) single nucleotide variant Uncertain significance rs146467199 GRCh38 Chromosome 2, 135809061: 135809061
39 LCT NM_002299.3(LCT): c.3286G> A (p.Ala1096Thr) single nucleotide variant Uncertain significance rs146467199 GRCh37 Chromosome 2, 136566631: 136566631
40 LCT NM_002299.3(LCT): c.3285C> T (p.His1095=) single nucleotide variant Uncertain significance rs372534937 GRCh38 Chromosome 2, 135809062: 135809062
41 LCT NM_002299.3(LCT): c.3285C> T (p.His1095=) single nucleotide variant Uncertain significance rs372534937 GRCh37 Chromosome 2, 136566632: 136566632
42 LCT NM_002299.3(LCT): c.3006G> A (p.Arg1002=) single nucleotide variant Uncertain significance rs114815229 GRCh38 Chromosome 2, 135809341: 135809341
43 LCT NM_002299.3(LCT): c.3006G> A (p.Arg1002=) single nucleotide variant Uncertain significance rs114815229 GRCh37 Chromosome 2, 136566911: 136566911
44 LCT NM_002299.3(LCT): c.2883C> T (p.Ala961=) single nucleotide variant Uncertain significance rs140994860 GRCh38 Chromosome 2, 135809464: 135809464
45 LCT NM_002299.3(LCT): c.2883C> T (p.Ala961=) single nucleotide variant Uncertain significance rs140994860 GRCh37 Chromosome 2, 136567034: 136567034
46 LCT NM_002299.3(LCT): c.2763G> A (p.Ala921=) single nucleotide variant Uncertain significance rs116951780 GRCh38 Chromosome 2, 135809584: 135809584
47 LCT NM_002299.3(LCT): c.2763G> A (p.Ala921=) single nucleotide variant Uncertain significance rs116951780 GRCh37 Chromosome 2, 136567154: 136567154
48 LCT NM_002299.3(LCT): c.1461G> A (p.Ala487=) single nucleotide variant Uncertain significance rs146206234 GRCh38 Chromosome 2, 135817587: 135817587
49 LCT NM_002299.3(LCT): c.1461G> A (p.Ala487=) single nucleotide variant Uncertain significance rs146206234 GRCh37 Chromosome 2, 136575157: 136575157
50 LCT NM_002299.3(LCT): c.655G> A (p.Val219Ile) single nucleotide variant Benign rs3754689 GRCh38 Chromosome 2, 135833176: 135833176

Expression for Lactase Deficiency, Congenital

Search GEO for disease gene expression data for Lactase Deficiency, Congenital.

Pathways for Lactase Deficiency, Congenital

Pathways related to Lactase Deficiency, Congenital according to KEGG:

37
# Name Kegg Source Accession
1 Galactose metabolism hsa00052

GO Terms for Lactase Deficiency, Congenital

Sources for Lactase Deficiency, Congenital

3 CDC
7 CNVD
9 Cosmic
10 dbSNP
11 DGIdb
17 ExPASy
19 FMA
28 GO
29 GTR
30 HGMD
31 HMDB
32 HPO
33 ICD10
34 ICD10 via Orphanet
35 ICD9CM
36 IUPHAR
37 KEGG
38 LifeMap
40 LOVD
42 MedGen
44 MeSH
45 MESH via Orphanet
46 MGI
49 NCI
50 NCIt
51 NDF-RT
54 NINDS
55 Novoseek
57 OMIM
58 OMIM via Orphanet
62 PubMed
64 QIAGEN
69 SNOMED-CT via HPO
70 SNOMED-CT via Orphanet
71 TGDB
72 Tocris
73 UMLS
74 UMLS via Orphanet
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