Evidence · Replicated

What the research found

In the cited research, the C allele at rs4654748 was associated with lower circulating vitamin B6 concentrations in the studied cohorts.

TT: Higher average
CT: Middle
CC: Lower average

Modest effect

What the study found

In the study, each copy went with blood level of this vitamin about 1.45 ng/mL lower on average.

Italian adults (InCHIANTI discovery and Progetto Nutrizione replication) · 1,864 people · Results paragraph on vitamin B6 and Table 2 (four-cohort meta-analysis column)

Evidence: Genome-wide association with independent replication
Who was studied: Italian InCHIANTI discovery and Progetto Nutrizione replication cohorts

1000 Genomes Project

How common each genotype is

How common each genotype is in the 1000 Genomes Project, by region
Region	TTHigher average	CTMiddle	CCLower average
All regions2,504 people	18%	39%	43%
Africa661 people	<1%	12%	88%
The Americas347 people	20%	47%	33%
East Asia504 people	32%	53%	16%
Europe503 people	22%	50%	28%
South Asia489 people	21%	48%	32%

Among the 2,504 people of the 1000 Genomes Project, in five world regions. These percentages describe groups of people, never anyone’s chance of having a trait.

Ancient genomes

Through time

How often the studied letter was read in ancient people, era by era, in the region chosen.

Region

Through time: Europe
Before farmingbefore 6500 BC	72%38 of 53 copies read
First farmers6500 to 3000 BC	42%370 of 873 copies read
Bronze Age3000 to 1200 BC	49%389 of 797 copies read
Iron Age and Antiquity1200 BC to AD 600	47%507 of 1,086 copies read
Middle AgesAD 600 to 1500	45%251 of 560 copies read
Today1000 Genomes	53%529 of 1,006 copies

Neanderthal and Denisovan genomes

Altai Neanderthal: 2 copies
Vindija Neanderthal: 2 copies
Chagyrskaya Neanderthal: 2 copies
Denisovan: 2 copies

For most ancient people only one of their two copies can be read, so these counts are copies read, not people. Close relatives, repeated samples and samples the archive marks as unreliable are left out. Damage in old DNA can fake this letter, so it is counted only from samples treated to remove that damage and from high-quality genomes. Ancient genomes from the Allen Ancient DNA Resource (AADR v66): 15,136 people.

rs4654748

The marker

Gene or region: ALPL region
Marker: rs4654748
Location: Chromosome 1 · GRCh37 21,786,068 · GRCh38 21,459,575
Letters studied: C and T, with C as the studied allele

A DNA Traits report reads this marker in your raw DNA file and shows which of the three genotypes is yours, with how common it is. It counts the copies of the studied allele; it does not measure the trait itself.

Marker: ALPL region · rs4654748
Location: Chromosome 1 · GRCh37 21,786,068 · GRCh38 21,459,575
Studied allele: C
Published statistic: beta -1.45 ng/mL per C allele (SE 0.28), P 8.30e-18, N 1,864; discovery -1.38 (SE 0.32), P 1.21e-8; replication -1.668 (SE 0.56), P 2.08e-11; Table 2 (Results paragraph on vitamin B6 and Table 2 (four-cohort meta-analysis column))
1000 Genomes Project phase 3, people with 0, 1 and 2 copies: All regions 446 / 988 / 1070 · Africa 4 / 77 / 580 · The Americas 69 / 162 / 116 · East Asia 159 / 265 / 80 · Europe 113 / 251 / 139 · South Asia 101 / 233 / 155

See this card in the sample report

Limits

What it cannot tell you

This common association concerns a blood vitamin B6 biomarker. It is not a test for a rare ALPL-related disorder and does not measure vitamin B6 absorption. Only the studied C/T allele pair is interpreted. It cannot tell you a current vitamin B6 level, is not a test for deficiency and cannot choose a diet, supplement or dose.

Genome-wide Association Study of Vitamin B6, Vitamin B12, Folate, and Homocysteine Blood Concentrations (Tanaka et al., 2009)

The same topic

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