SLC6A19

Chr 5AR

solute carrier family 6 member 19

Also known as: B0AT1, HND

NCBI Gene: 340024 ENSG00000174358 UniProt: Q695T7 OMIM: 608893

The protein functions as a sodium-dependent transporter that mediates resorption of neutral amino acids across the apical membrane of renal and intestinal epithelial cells, requiring accessory proteins (CLTRN in kidney, ACE2 in intestine) for proper cell surface expression and activity. Mutations cause Hartnup disorder, an autosomal recessive condition characterized by pellagra-like symptoms, cerebellar ataxia, and psychosis. The gene shows very low constraint against loss-of-function variants (LOEUF 1.42), consistent with the recessive inheritance pattern where heterozygous carriers are typically unaffected.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a system B(0) transmembrane protein that actively transports most neutral amino acids across the apical membrane of epithelial cells. Mutations in this gene may result in Hartnup disorder, an inherited disease with symptoms such as pellagra, cerebellar ataxia, and psychosis. The expression and function of B0AT1 (SLC6A19) in intestinal cells depends on the presence of the accessory protein angiotensin-converting enzyme 2 (ACE2) which, among other functions, acts as a chaperone for membrane trafficking of B0AT1. The ACE2 is also the cellular receptor for severe acute respiratory syndrome-coronavirus (SARS-CoV) and for SARS-CoV-2 that is causing the coronavirus 2019 (COVID-19) pandemic [provided by RefSeq, Jul 2020]

OMIM ResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

Hartnup disorderMIM #234500

UniProtHyperglycinuria

UniProtIminoglycinuria

Clinical highlights

Gene–disease validity (ClinGen)

Definitive · Hartnup disease · AR · ClinGen 2020

Interpreting a novel variant

Loss of function is the curated mechanism (Gene2Phenotype), though the gene is not strongly LoF-constrained in the population — weigh truncating variants against that tolerance.Curated gene-level mechanism — a prior for triage, not a per-variant call.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

—

LOEUF

LOF

Mechanism· G2P

Some data sources returned errors (1)

gnomad: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD

Constraint data not available from gnomAD.

Background carrier burden — how many people carry a rare variant somewhere in SLC6A19?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 61

873 rare PASS variants

Rare truncating (LoF)

1 in 570

130 rare PASS variants

Rare synonymous (reference)

1 in 51

409 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC6A19. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 73	1 in 560
South Asian	~43k	1 in 47	1 in 760
Remaining (unassigned)	~30k	1 in 59	1 in 740
European (Finnish)	~27k	1 in 220	1 in 360
Admixed American	~22k	1 in 37	1 in 830
African / African American	~21k	1 in 50	1 in 430
East Asian	~20k	1 in 49	1 in 560
Ashkenazi Jewish	~13k	1 in 200	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 42	≈ 1 in 1,400

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 12 of 12 coding exons well covered in gnomAD exomes. Genomes: 11 of 12 (exon 5 below).? see exons ↓