S100A7A

protein-coding

S100 calcium binding protein A7A, the group of S100 calcium binding proteins|EF-hand domain containing

Gene summary

Enables identical protein binding activity. Predicted to be involved in endothelial cell migration. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

S100A15
S100A7L1

MANE transcript

NM_176823.4

Inheritance

—

ClinVar variants

U:23B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.87

Max pathogenic AF

—

Genomic locus

chr1:153,416,520-153,423,222

External References & Databases

Ensembl (ENSG00000184330)

Transcript & Mutation Effects

hg38 • Region Span ~6.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to S100A7A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 28

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_176823.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			23 clinvar	5 clinvar		28
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	6	0	29

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_176823.4	RefSeq	NP_789793.1	2	MANE Select
ENST00000368729.9	Ensembl	ENSP00000357718.3	2	MANE Select
ENST00000329256.2	Ensembl	ENSP00000329008.2	2	Standard
ENST00000329256.3	Ensembl	ENSP00000329008.2	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Antimicrobial peptides
Innate Immune System
Immune System
Metal sequestration by antimicrobial proteins

Molecular Function

calcium ion binding
protein self-association
transition metal ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368729
Coding exons: 2
Length: 6702
Individuals with no LoFs: 125522
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125523
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.27	84	57.0	1.47	0.00000292	679
Missense (PolyPhen)		16	12.289	1.302		178
Synonymous	-1.28	32	24.0	1.33	0.00000158	173
Loss of Function	-1.02	3	1.61	1.87	6.72e-8	21

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in epidermal differentiation and inflammation and might therefore be important for the pathogenesis of psoriasis and other diseases.;

Intolerance Scores

LoFtool: 0.540
RVIS EVS: 0.75
RVIS percentile EVS: 86.57

Essentials

Essential (CRISPR): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0440

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium