SLC30A4

Chr 15

solute carrier family 30 member 4

Also known as: ZNT4, znT-4

NCBI Gene: 7782 ENSG00000104154 UniProt: O14863

Zinc is the second most abundant trace metal in the human body. It is an essential element, serving both a structural role, as in the formation of zinc fingers in DNA-binding proteins, and a catalytic role in metalloenzymes, such as pancreatic carboxypeptidases (e.g., MIM 114852), alkaline phosphatases (e.g., MIM 171760), various dehydrogenases, and superoxide dismutases (e.g., MIM 147450). SLC30A4, or ZNT4, belongs to the ZNT family of zinc transporters. ZNTs are involved in transporting zinc out of the cytoplasm and have similar structures, consisting of 6 transmembrane domains and a histidine-rich cytoplasmic loop (Huang and Gitschier, 1997 [PubMed 9354792]).[supplied by OMIM, Mar 2008]

Research

ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.58

LOEUF

Multiple*

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.58LOEUF

pLI 0.115

Z-score 2.86

OE 0.28 (0.14–0.58)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

1.05Z-score

OE missense 0.81 (0.72–0.91)

190 obs / 235.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.28 (0.14–0.58)

0≤0.351.4

Missense OE?0.81 (0.72–0.91)

0≤0.61.4

Synonymous OE?0.84

0≤1.21.6

LoF obs/exp: 5 / 18.2Missense obs/exp: 190 / 235.4Syn Z: 1.19

Background carrier burden — how many people carry a rare variant somewhere in SLC30A4?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 150

469 rare PASS variants

Rare truncating (LoF)

1 in 4,600

52 rare PASS variants

Rare synonymous (reference)

1 in 330

193 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SLC30A4. 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 200	1 in 4,300
South Asian	~43k	1 in 210	1 in 4,800
Remaining (unassigned)	~30k	1 in 150	≈ 1 in 15,000
European (Finnish)	~27k	1 in 490	≈ 1 in 8,800
Admixed American	~22k	1 in 170	1 in 3,700
African / African American	~21k	1 in 160	≈ 1 in 6,000
East Asian	~20k	1 in 180	≈ 1 in 9,900
Ashkenazi Jewish	~13k	1 in 360	≈ 1 in 13,000
Middle Eastern	~2,884	1 in 180	≈ 1 in 2,300

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): 5 of 7 coding exons well covered in gnomAD exomes; exons 6, 7 marginal. Genomes: all 7.? see exons ↓