S100Z

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

Basic information

Region (hg38): 5:76850000-76921650

Links

ENSG00000171643 ∙ NCBI:170591 ∙ OMIM:610103 ∙ HGNC:30367 ∙ Uniprot:Q8WXG8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the S100Z gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100Z gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in S100Z

This is a list of pathogenic ClinVar variants found in the S100Z region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-76875387-G-T		not specified	Uncertain significance (Mar 19, 2024)
5-76875438-T-C		not specified	Uncertain significance (Oct 27, 2022)
5-76877782-G-A		not specified	Uncertain significance (Jul 25, 2023)
5-76877828-A-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100Z	protein_coding	protein_coding	ENST00000317593	2	71650

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0132	0.679	124385	1	413	124799	0.00166

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.141	56	53.1	1.05	0.00000264	660
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000740	0.000739
Ashkenazi Jewish	0.00	0.00
East Asian	0.00823	0.00821
Finnish	0.000989	0.000974
European (Non-Finnish)	0.00182	0.00180
Middle Eastern	0.00823	0.00821
South Asian	0.000360	0.000360
Other	0.00185	0.00182

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.712
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.16

Haploinsufficiency Scores

• pHI: 0.109
• hipred: N
• hipred_score: 0.460
• ghis: 0.403

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100z

Gene ontology

• Biological process: biological_process
• Molecular function: calcium ion binding;protein binding;protein homodimerization activity