gene pfcrt

pfcrt

Locus: PF3D7_0709000 (pfcrt)

Plasmodium falciparum chloroquine transporter (PfCRT), encoded by pfcrt gene, is a transmembrane protein located at digestive vacuole membrane. Mutation at amino acid residues 76 has been an important marker of chloroquine resistance.

Table 1 Frequent mutations in Pfcrt

Codon	Wild-type	Mutation
72	C	S,Y
73	V	-
74	M	I
75	N	D,E
76	K	T,K

Haplotype Distribution

The following table demonstrated the distribution of PfCRT haplotypes in different geographical subcontinents. This table used the data from Version 6.0 of MalariaGEN Plasmodium falciparum Community Project .

Table 2 Haplotype distribution of PfCRT among different geographical locations

Haplotypea	SAM	EAF	CAF	WAF	SAS	ESEA	WSEA	OCE	Total
CVIDT	0	0	0	0	0	237	0	0	237
CVIET	2	160	314	975	157	1493	1285	0	4386
CVMET	61	0	0	0	0	0	0	0	61
CVMNK	1	711	165	1275	8	43	9	2	2214
CVMNT	21	0	0	0	0	0	0	0	21
SVMNT	12	0	0	0	0	0	0	198	210
YVIET	0	0	0	0	0	4	0	0	4
Total	97	871	479	2250	165	1777	1294	200	7133

^aRepresents amino acids, left-to-right, at codons 72, 73, 74, 75 and 76, respectively

SAM = South America; EAF = East Africa; CAF = Central Africa; WAF = West Africa;

SAS = South Asia; ESEA = East South-East Asia; WSEA = West South-East Asia; OCE = Oceania

Associations between alleles

To impute the missing codons in PfCRT, the associations between amino acids at position 72, 73, 74, 75 and 76 were assessed to generate the imputation rules using the data from MalariaGEN Plasmodium falciparum Community Project version 6.0.

Codons 72 and 74

There is a significant association between PfCRT codons 72 and 74 in the parasites from all regions (see Table 3). The results suggested the following imputation rule:

1. 72S predicts M74

Table 3 Contingency table of co-occurrence between codons 72 and 74

All regions	C72	72S	72Y	Total
74I	4838	0	4	4842
M74	2362	211	0	2573
Total	7200	211	4	7415

Fisher's exact test : P < 0.01

Noted that 72S mutation was distributed only in South America and Oceania and 72Y mutation occurred in Southeast Asia. Disregarding certain regions could suggest the additional rules:

1. Disregarding SAM and OCE: M74 predicts C72
2. Disregarding SAM, OCE, WSEA and ESEA: 74I predicts C72

Codons 72 and 75

There is a significant association between PfCRT codons 72 and 75 in the parasites from all regions (see Table 4). The results suggested the following imputation rules:

1. 75D predicts C72
2. 72S predicts N75

Table 4 Contingency table of co-occurrence between codons 72 and 75

All regions	C72	72S	72Y	Total
75D	237	0	0	237
75E	4662	0	4	4666
N75	2301	211	0	2512
Total	7200	211	4	7415

Fisher's exact test : P < 0.01

Noted that 72S mutation was distributed only in South America and Oceania and 72Y mutation occurred in Southeast Asia. Disregarding certain regions could suggest the additional rules:

1. Disregarding SAM and OCE: N75 predicts C72
2. Disregarding SAM, OCE, WSEA and ESEA: 75E predicts C72

Codons 72 and 76

There is a significant association between PfCRT codons 72 and 76 in the parasites from all regions (see Table 5). The results suggested the following imputation rules:

1. K76 predicts C72
2. 72S predicts 76T

Table 5 Contingency table of co-occurrence between codons 72 and 76

All regions	C72	72S	72Y	Total
K76	2280	0	0	2280
76T	4920	211	4	5135
Total	7200	211	4	7415

Fisher's exact test : P < 0.01

Noted that 72S mutation was distributed only in South America and Oceania and 72Y mutation occurred in Southeast Asia. Disregarding certain regions could suggest the additional rules:

1. Disregarding SAM, OCE, WSEA, and ESEA: 76T predicts C72

Codons 74 and 75

There is a significant association between PfCRT codons 74 and 75 in the parasites from all regions (see Table 6). The results suggested the following imputation rules:

1. 75D predicts 74I
2. N75 predicts M74

Table 6 Contingency table of co-occurrence between codons 74 and 75

All regions	74I	M74	Total
75D	237	0	237
75E	4605	61	4666
N75	0	2512	2512
Total	4842	2573	7415

Fisher's exact test : P < 0.01

When disregarding the parasites from South America (SAM), these following imputation rules are suggested (see Table 7):

1. 75E predicts 74I
2. M74 predicts N75

Table 7 Contingency table of co-occurrence between codons 74 and 75 when disregarding the parasites from South America

All except South America	74I	M74	Total
75D	237	0	237
75E	4388	0	4388
N75	0	2411	2411
Total	4625	2411	7036

Fisher's exact test : P < 0.01

Disregarding the parasites from South America and Southeast Asia (SAM, WSEA and ESEA) suggested this additional rule:

1. 74I predicts 75E

Codons 74 and 76

There is a significant association between PfCRT codons 74 and 76 in the parasites from all regions (see Table 8). The results suggested the following imputation rules:

1. K76 predicts M74
2. 74I predicts 76T

Table 8 Contingency table of co-occurrence between codons 74 and 76

All regions	74I	M74	Grand Total
K76	0	2280	2280
76T	4842	293	5135
Total	4842	2573	7415

Fisher's exact test : P < 0.01

When disregarding the parasites from South America and Oceania (SAM and OCE), these following imputation rules are suggested (see Table 9):

1. M74 predicts K76
2. 76T predicts 74I

Table 9 Contingency table of co-occurrence between codons 74 and 76 when disregarding the parasites from South America and Oceania

All regions except South America and Oceania	74I	M74	Total
K76	0	2211	2211
76T	4625	0	4625
Total	4625	2211	6836

Fisher's exact test : P < 0.01

Codons 75 and 76

There is a significant association between PfCRT codons 75 and 76 in the parasites from all regions (see Table 10). The results suggested the following imputation rules:

1. K76 predicts N75
2. 75D predicts 76T
3. 75E predicts 76T

This additional rule is suggested when disregarding the parasites from South America and Oceania (SAM and OCE):

1. N75 predicts K76

Table 10 Contingency table of co-occurrence between codons 75 and 76

All regions	75D	75E	N75	Total
K76	0	0	2280	2280
76T	237	4666	232	5135
Total	237	4666	2512	7415

Fisher's exact test : P < 0.01

Imputation Rules

Summary of imputation rules generated from association among PfCRT codons in MalariaGEN Plasmodium falciparum Community Project dataset.

Table 11 Imputation rules for predicting PfCRT haplotype

Region	Inputa	Outputa	Coding
Any	S V - - -	S V M N T	if(crt_72[C] == "S") {crt_74[M] <- "M" & crt_75[N] <- "N" & crt_76[K] <- "T"}
Any	- V I - -	- V I - T	if(crt_74[M] == "I") {crt_76[K] <- "T"}
Any	- V - D -	C V I D T	if(crt_75[N] == "D") {crt_72[C] <- "C" & crt_74[M] <- "I" & crt_76[K] <- "T"}
Any	- V - E -	- V - E T	if(crt_75[N] == "E") {crt_76[K] <- "T"}
Any	- V - N -	- V M N -	if(crt_75[N] == "N") {crt_75[N] <- "N"}
Any	- V - - K	C V M N K	if(crt_76[K] == "K") {crt_72[C] <- "C"& crt_74[M] <- "M" & crt_75[N] <- "N"}
WAF, CAF, EAF, SAS	- V I - -	C V I E T	if(crt_74[M] == "I") {crt_72[C] <- "C" & crt_75[N] <-"E" & crt_76[K] <- "T"}
WSEA, ESEA	- V - E -	- V I E T	if(crt_75[N] == "E") {crt_74[M] <- "I" & crt_76[K] <- "T"}
WAF, CAF, EAF, SAS	- V - E -	C V I E T	if(crt_75[N] == "E") {crt_72[C] <- "C" & crt_74[M] <- "I" & crt_76[K] <- "T"}
WAF, CAF, EAF, SAS, WSEA, ESEA	- V - N -	C V M N K	if(crt_75[N] == "N") {crt_72[C] <- "C" & crt_74[M] <- "M" & crt_76[K] <- "K"}
OCE	- V M - -	- V M N -	if(crt_74[M] == "M") {crt_75[N] <- "N"}
WAF, CAF, EAF, SAS, WSEA, ESEA	- V M - -	C V M N K	if(crt_74[M] == "M") {crt_72[C] <- "C" & crt_75[N] <- "N" & crt_76[K] <- "K"}
WSEA, ESEA	- V - - T	- V I - T	if(crt_76[K] == "T") {crt_74[M] <- "I"}
WAF, CAF, EAF, SAS	- V - - T	C V I E T	if(crt_76[K] == "T") {crt_72[C] <- "C" & crt_74[M] <- "I" & crt_75[N] <- "E"}

^aRepresents amino acids, left-to-right, at codons 72, 73, 74, 75 and 76, respectively

Association between K76T and markers for chloroquine resistance

K76T mutation has been used as a marker for chloroquine resistance, however, single pfcrt K76T mutation is not sufficient to cause altered chloroquine susceptibility. The data from Version 6.0 of MalariaGEN Plasmodium falciparum Community Project was assessed for the association between K76T mutation and other additional markers for chloroquine resistance, including residues 75, 220 and 326. Table 12 and table 13 suggested significant association between K76T mutation and at least 1 additional maker of high-level of chloroquine resistance. We can imply that K76T is a predictor for these additional chloroquine-resistant markers.

Table 12 Contingency table of co-occurrence between codons 76 and chloroquine-resistant markers codon 75, 220 and 326

	K76	76T	Total
N75+A220+N326	2056	0	2056
N75+220S+N326	3	0	3
75D+220S+N326	0	210	210
75E+A220+N326	0	2	2
75E+220S+N326	0	1658	1658
75E+220S+326S	0	2060	2060
75N+220S+326D	0	222	222
Total	2059	4152	6211

Table 13 Contingency table of co-occurrence between codons 76 and additional markers for chloroquine resistance

	K76	76T	Total
No additional resistant markers	2056	0	2056
With at least 1 additional marker	3	4152	4155
Total	2059	4152	6211

Fisher's exact test : P < 0.01

See also

• Chloroquine