S100A14

Chr 1

S100 calcium binding protein A14

Also known as: BCMP84, S100A15

NCBI Gene: 57402 ENSG00000189334 UniProt: Q9HCY8 OMIM: 607986

This gene encodes a member of the S100 protein family which contains an EF-hand motif and binds calcium. The gene is located in a cluster of S100 genes on chromosome 1. Levels of the encoded protein have been found to be lower in cancerous tissue and associated with metastasis suggesting a tumor suppressor function (PMID: 19956863, 19351828). [provided by RefSeq, Dec 2011]

OMIM Research

OMIM ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.81

LOEUF

Multiple*

Mechanism· predicted

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.81LOEUF

pLI 0.002

Z-score 0.10

OE 0.95 (0.46–1.81)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.22Z-score

OE missense 1.08 (0.89–1.33)

66 obs / 61.1 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.95 (0.46–1.81)

0≤0.351.4

Missense OE?1.08 (0.89–1.33)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 4 / 4.2Missense obs/exp: 66 / 61.1Syn Z: 0.13

Background carrier burden — how many people carry a rare variant somewhere in S100A14?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 430

127 rare PASS variants

Rare truncating (LoF)

1 in 7,700

21 rare PASS variants

Rare synonymous (reference)

1 in 660

56 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for S100A14. 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 460	1 in 9,600
South Asian	~43k	1 in 240	≈ 1 in 11,000
Remaining (unassigned)	~30k	1 in 390	1 in 950
European (Finnish)	~27k	1 in 5,300	none seen
Admixed American	~22k	1 in 230	1 in 2,800
African / African American	~21k	1 in 530	≈ 1 in 21,000
East Asian	~20k	1 in 360	≈ 1 in 6,600
Ashkenazi Jewish	~13k	1 in 1,300	none seen
Middle Eastern	~2,884	≈ 1 in 720	none seen

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): All 3 coding exons well covered in gnomAD exomes and genomes.? see exons ↓