S100Z

protein-coding

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

Gene summary

Members of the S100 protein family contain 2 calcium-binding EF-hands and exhibit cell-type specific expression patterns. For additional background information on S100 proteins, see MIM 114085.[supplied by OMIM, Mar 2008]

MANE transcript

NM_130772.4

Inheritance

—

ClinVar variants

U:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr5:76,850,001-76,921,650

External References & Databases

Ensembl (ENSG00000171643)

Transcript & Mutation Effects

hg38 • Region Span ~71.6 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 S100Z variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_130772.4. 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						0
missense			9 clinvar			9
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	10	0	0	10

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_130772.4	RefSeq	NP_570128.2	2	MANE Select
ENST00000317593.9	Ensembl	ENSP00000320430.4	2	MANE Select
NM_001437778.1	RefSeq	NP_001424707.1	2	Standard
NM_001437779.1	RefSeq	NP_001424708.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

calcium ion binding
protein binding
protein homodimerization activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000317593
Coding exons: 2
Length: 71650
Individuals with no LoFs: 124385
Homozygous LoFs: 1
Heterozygous LoFs: 413
Defined: 124799
p: 0.00166

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.141	56	53.1	1.05	0.00000264	660
Missense (PolyPhen)		16	14.489	1.1043		218
Synonymous	0.571	18	21.4	0.843	0.00000120	175
Loss of Function	0.560	3	4.24	0.707	2.20e-7	52

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00026	rare
Latino/Admixed American	0.00048	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0082	0.0082	notable
Finnish	0.00099	0.00097	rare
European (Non-Finnish)	0.0018	0.0018	notable
South Asian	0.00036	0.00036	rare
Other	0.0019	0.0018	notable

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.712
RVIS EVS: 0.46
RVIS percentile EVS: 78.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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