Ruan et al. BMC Medical Genetics(2020) 21:221
https://doi.org/10.1186/s12881-020-01158-z

CASE REPORTOpen Access

Hereditary intrinsic factor deficiency inChina caused by a novel mutation in the
intrinsic factor gene—a case report
Jing Ruan, Bing Han* , Junling Zhuang, Miao Chen, Fangfei Chen, Yuzhou Huang and Wenzhe Zhou

Abstract
Background: Hereditary intrinsic factor deficiency is a rare disease characterized by cobalamin deficiency with the lackof gastric intrinsic factor because of gastric intrinsic factor (GIF) mutations. Patients usually present with cobalamin
deficiency without gastroscopy abnormality and intrinsic factor antibodies.
Case presentation: A Chinese patient presented with recurrent severe anemia since age 2 with low cobalamin level
and a mild elevation of indirect bilirubin. The hemoglobin level normalized each time after intramuscular vitamin B12
injection. Gene test verified a c.776delA frame shift mutation in exon 6 combined with c.585C > A nonsense earlytermination mutation in exon 5 of GIF which result in the dysfunction of gastric intrinsic factor protein. The hereditary
intrinsic factor deficiency in literature was further reviewed and the ancestry of different mutation sites were discussed.
Conclusions: A novel compound heterozygous mutation of GIF in a Chinese patient of hereditary intrinsic factor
deficiency was reported. It was the first identified mutation of GIF in East-Asia and may indicate a new ancestry.
Keywords: Megaloblastic anemia, Cobalamin deficiency, Intrinsic factor

Background
Vitamin B12 or cobalamin deficiency is characterized bymegaloblastic anemia with neurological problems andcan be caused by numerous acquired and inherited diseases [1]. Decreased intake, impaired gastric absorption
including pernicious anemia and gastrectomy, impaired
intestinal absorption caused by parasites infection arecommon acquired causes. As for inherited diseases, themechanisms vary from impaired cobalamin absorption,
defects of cobalamin transport to failure of cellular cobalamin metabolism. Two hereditary diseases have beenfound to cause cobalamin malabsorption including
Imerslund-Grasbeck syndrome (IGS) and hereditary intrinsic factor deficiency (IFD) [2].

* Correspondence: rjgrass@126.com
Department of Hematology, Peking Union Medical College, Hospital, Chinese
Academy of Medical Sciences, No.1 Shuaifuyuan, Dongcheng District, Beijing
100730, China

IFD is caused by homozygous or compound heterozygous mutation in the gene of gastric intrinsic factor on
chromosome 11q12. It presents in early childhood withthe lack of gastric intrinsic factor, while the gastric acidsecretion is normal and no autoantibody to intrinsic factor is found. It is a rare disease mostly occurring in theEurope [3]. Here we present a Chinese family identified
to have hereditary intrinsic factor deficiency with a new
mutation site in GIF that has not been reported.

Case presentation
Clinical manifestation

The proband was a 16-year-old Chinese boy with a history of patent ductus arteriosus. The child was initiallyevaluated for severe anemia at the age of 2. Severe megaloblastic anemia, low cobalamin level and a mild elevation of indirect bilirubin were found. The hemoglobin
level normalized after intramuscular vitamin B12 injection and oral folate with unknown dosage. He did not© The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License,
which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give
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Ruan et al. BMC Medical Genetics(2020) 21:221

have severe symptoms the following years. At age 8, he
was admitted to the hospital for the recurrence ofanemia induced by upper airway infection. He also had
jaundice and tea-colored urine. The hemoglobin was
57 g/L, mean cell volume was 97.8fL, and the cobalaminlevel was 80 pg/mL. Hemolytic anemia was also foundwith the indirect bilirubin to be 43.0umol/L and lactate
dehydrogenase to be 1832U/L. Rous test, Coombs test,
erythrocyte osmotic fragility test, glucose-6-phosphate
dehydrogenase activity and the count of CD55/CD59
negative cells were normal. The ultrasound of the spleen
showed a mild enlargement. Bone marrow indicatedmegaloblastic erythroid hyperplasia. He was treated withintramuscular injection of vitamin B12 at the dosage of
0.5 mg every other day and his hemoglobin increased to
114 g/L. The patient had recurrent anemia 4 times fromage 10 to 16 and the hemoglobin regained normal afterB12 supplement. He came to our hospital for further
examination. We found the antibody of intrinsic factor
was negative and his gastroscope was normal. Since his
grandmother and his father also had mild anemia, cobalamin concentration was then tested, and they wereboth diagnosed to have vitamin B12 deficiency. (Fig. 1).
Therefore, hereditary disease was further suspected, andwe performed genome sequencing to convince it.
Analysis of genome sequencing

Genomic DNA was isolated from the peripheral bloodof the patient. SeqCap EZ Choice XL Library (Roche
NimbleGen) was used to hybridize the exons and adjacent intron regions (50 bp) of 238 genes related to hereditary hematological diseases. After amplification andpurification, high-throughput sequencing was performedby Illumina. Analysis was performed using the hg19 annotation information provided by UCSC. Genomic DNA
samples of the patient’s parents and grandparents werethen isolated for validation of the identified mutations

Fig. 1 Family tree of the proband

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by Sanger sequencing. The patient had compound heterozygous mutation in GIF gene (Fig. 2). There was ac.776delA mutation combined with c.585C > A mutationon the other allele. c.776delA (p.Q259Rfs*17) is a frame
shift mutation in exon 6 caused by 1 bp deletion which
would result in abnormal protein translation. It was also
found in father and grandmother of the proband.
c.585C > A (p.Y195X) is a nonsense mutation in exon 5that would lead to the early termination of the gene coding protein and was also detected in his mother. Since
there are reports for mutations of the downstream coding sites that could result in abnormal function of thegastric intrinsic factor, these two mutations are boththought to cause pathological changes.

Discussion and conclusions
Juvenile cobalamin deficiency usually presents with various
hematological problems ranging from mild weakness to liftthreatening anemia. Patients may present with yellow skincaused by combined anemia and jaundice. Rate of infectionis also increased due to neutropenia, thrombocytopenia andmegaloblastic anemia. The neurologic abnormalities are alsovariable and may not be recognized without attention.
Growth retardation and learning difficulties are more commonly seen in the juveniles [4]. Patients may also have dementia, psychological problems and neurodegeneration of
the spinal cord.
Although inborn cobalamin deficiency is rare, with socialand economic development, dietary and infectious causes ofcobalamin deficiency are decreased and the prevalence ofinherited cobalamin deficiency has increased [5]. Inborn errors affecting intestinal cobalamin absorption, transport ofcobalamin in blood, uptake of cobalamin by cells or intracellular cobalamin metabolism could all cause cobalamin deficiency. As for hereditary cobalamin malabsorption, IGS
caused by CUBN or AMN mutations and IFD caused by GIF
mutations are most common ones. Schilling test was used in
the past to differentiate IFD from IGS and has been
obsoleted because of invasiveness and lack of access to theradiolabeled vitamin B12. Genetic testing is now available forthe validation and classification of the inherited cobalaminmalabsorption. Tanner et al. 2012 [3] observed 22%, 42%,
36% of the mutations in GIF, CUBN and AMN genes respectively in a large genetic screening study of 154 families
or patients with hereditary deficiency of vitamin B12
absorption.
Hereditary intrinsic factor deficiency is characterized bycobalamin deficiency with the lack of gastric intrinsic factor because of GIF mutations. The gastric acid secretionand gastroscopy are often normal and no autoantibodies
to intrinsic factor should be found. We summarized themutations in GIF from previous literature in Table 1. The
first report with identified genetic mutations was in 2004
[6]. Yassin et al. [6] identified a 4-base deletion (c183_

Ruan et al. BMC Medical Genetics(2020) 21:221

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Fig. 2 Sanger validation of the compound heterozygous mutation in GIF gene

Table1 Summary mutations in the GIF gene according to previous literature (add to page 5 line 19)
DNA mutation

RegionGenotype Predicted consequence

References

Originc.79 + 1G > A

intron 1

hom

splice site mutation

Tanner et al. 2005 [5], Tanner et al.
2012 [3]France, Norway,
USAc.79 + 1G > A & del Intron 8
to distal of 3′-end

intron 1 &delcomp het

splice site mutation & partial
gene deletion

Tanner et al. 2012 [3]Norwayc.79 + 1G > A & c.137C > T

intron 1 &exon 2comp het

splice site mutation &p.Ser46Leu

Tanner et al. 2012 [3]USA (Western
Europe?)c.79 + 1G > A & c.290 T > C

intron 1 &exon 3comp het

splice site mutation &p.Met97Thr

Overgaard et al. 2010 [10]USA (Western
Europe?)c.79 + 1G > A & c.673A > C

intron 1 &exon 5comp het

splice site mutation &p.Ser225Arg

Tanner et al. 2012 [3]Siberiac.80-1G > A

intron 1

hom

splice site mutation

Tanner et al. 2005 [5]Kuwaitic.137C > T

exon 2hom

p.Ser46Leu

Tanner et al. 2005 [5], Tanner et al.
2012 [3]Turkeyc.161delA

exon 2homp.Asn54fs

Tanner et al. 2005 [5]Turkeyc.183_186delGAAT

exon 2

hom

p.Met61fs

Yassin et al. 2004 [6], Tanner et al. 2005 UK (Jamaican),[5], Ament et al. 2009 [8]African Americanc.183_186delGAAT &c.659 T > C

exon 2 &exon 5comp het

p.Met61fs & p.Ile220Thr

Ament et al. 2009 [8]USA (African,
European)c.256 + 2 T > G & c.659 T > C

intron 2 &exon 5comp het

splice site mutation &p.Ile220Thr

García Jiménez et al. 2008 [12]Spainc.290 T > C & ?

exon 3 & ? comp het

GIF c.290 T > C & FUT2
rs601338 461GG variant
c.431_438delAGAAGAAC &c.974_975insGexon 4 &exon7c.435_437delGAA & FUT2
rs601338 461GG variant

p.Met97Thr & ?

Tanner et al. 2012 [3]Finlandcomp het

GIF p.Met97Thr & FUT2
secretor variant

Chery et al. 2013 [13]Francecomp het

p.Gln144fs & p.Val325fs

Tanner et al. 2012 [3]Austriacomp het

p.Lys145_Asn146delinsAsn &FUT2 secretor variant

Chery et al. 2013 [13]Francec.469 T > C & ?

exon 4 & ? comp het

p.Phe157Leu & ?

Tanner et al. 2012 [3]USA (Lebanese)

c.685G > A

exon 5

p.Ala229Thr

Tanner et al. 2012 [3]Turkey, Germany(Lebanese)homc.938C > T & ?

exon 7 & ? comp het

p.Thr313Ile & ?

Tanner et al. 2012 [3]Israel (Arabic)

c.1073 + 5G > A

intron 7

hom

splice site mutation

Sturm et al. 2013 [11]USA (Chaldean)c.1175_1176insT

exon 8hom

p.Thr393fs

Tanner et al. 2005 [5]Turkeyc.1222G > A

exon 9hom

p.Glu408Lys

Lund Leunbach et al. 2011

DanishRuan et al. BMC Medical Genetics(2020) 21:221

186delGAAT, p.Met61fs) in exon 2 in an 11-year-old girlwith severe anemia and cobalamin deficiency. This homozygous mutation seems to originate in Africa and was also
reported by Tanner et al. 2005 [7] and Ament et al. 2009[8]. In Exon 2, another 2 homozygous mutation sites werealso found including the c.137C > T (p.Ser46Leu) andc.161delA (p.Asn54fs). There are also homozygous mutations in exon 5 (c.685G > A) [3], exon 8 (c.1175_1176insT)[7] and exon 9 (c.1222G > A) [9]. Intron mutations in the
splice site can also cause abnormal protein structures andfunctions. The most numerous one was c.79 + 1G > A mutation commonly found in Europe. Not only the homozygous mutation of this site but also in combination withother defects including a 3-terminal deletion in intron 8
and 3 different missense mutation sites (c.137C > T,
c.290 T > C [10], c.673A > C). c.80-1G > A in intron 1 [7]and c.1073 + 5G > A [11] homozygous mutations were reported respectively in West Asia area. There are also compound heterozygous mutations in two exons that generate
IFD [8, 12]. Notably, Chery et al. [13] reported 2 IFD family who carried FUT2 rs601338 secretor variants that impairs GIF secretion. This variant in combination with GIF
heterozygous mutation worsened the B12 status.
As for this patient, we found a c.776delA frame shift
mutation in exon 6 combined with c.585C > A nonsense
early termination mutation in exon 5 and the two mutation alleles were inherited from his parents respectively.
This compound heterozygous mutation caused the severe loss of function of the encoding gastric intrinsic factor protein and resulted in cobalamin deficiency. It was
the first identified novel mutation of GIF in East-Asia
and may indicate a new ancestry.
The treatment is merely vitamin B12 administration
by several routes including intramuscular and oral. Ourpatient recovered the hemoglobin level each time after
applying vitamin B12. In fact, treatment with life-longcobalamin administration at regular intervals is lifesaving and prevents further deterioration [14]. Early
diagnosis and detection by genetic methods in such juvenile cases followed by regular treatment may help
avoid severe hematological, neurological and developmental problems.
In summary, we identified a case diagnosed to be hereditary intrinsic factor deficiency firstly with genetic information in the East Asia. A novel compound heterozygous
mutation of GIF was reported which may indicate a different origin from previous literature.
Abbreviations
GIF: Gastric intrinsic factor; IGS: Imerslund-Grasbeck syndrome; IFD: Intrinsic
factor deficiency
Acknowledgements
We thank the proband and his family. Their cooperation and helpfulcomments contributed to this discovery.

Page 4 of 5

Authors’ contributions
BH designed the research study. JR analyzed the data and was a major
contributor in writing the manuscript. MC and JZ made the follow-up of thepatient and analyzed the clinical information. FC, YH and WZ collected the
medical record and analyzed the sequencing data. All authors revised andapproved the final manuscript.
Funding
This study was supported by grants from the Chinese Academy of Medical
Sciences innovation fund for medical sciences (2016-I2M-3–004), mainly usedin genome sequencing.
Availability of data and materials
The datasets generated and/or analyzed during the current study areavailable in the NCBI BioProject database under the accession number
PRJNA669950. The hg19 annotation dataset could be reached at https://
genome.ucsc.edu/.
Ethics approval and consent to participate
Written informed consent was obtained from the proband and his family
and the study was conducted in accordance with the Declaration of Helsinki.
The study protocol was approved by the Ethics Committee of Peking Union
Medical College Hospital.
Consent for publication
Written Consent for publication of the patient’s, the parents’ and the
grandparents’ clinical details and/or clinical images was obtained from theparents of the proband and the grandparents of the patient.
Competing interests
The authors declare that they have no conflict of interest.
Received: 22 July 2019 Accepted: 27 October 2020

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