S100G

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

Basic information

Region (hg38): X:16650158-16654670

Previous symbols: [ "CALB3" ]

Links

ENSG00000169906 ∙ NCBI:795 ∙ OMIM:302020 ∙ HGNC:1436 ∙ Uniprot:P29377 ∙ 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 S100G gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100G 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				1		1
non coding						0
Total	0	0	3	0	0

Variants in S100G

This is a list of pathogenic ClinVar variants found in the S100G region.

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

Position	Type	Phenotype	Significance	ClinVar
X-16651149-G-A			Likely benign (Dec 01, 2022)
X-16654406-G-A		not specified	Uncertain significance (Dec 20, 2023)
X-16654457-G-A		not specified	Uncertain significance (Jun 10, 2024)
X-16654475-A-C		not specified	Uncertain significance (Apr 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100G	protein_coding	protein_coding	ENST00000380200	2	4513

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.115	0.618	125411	8	15	125434	0.0000917

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	18	23.1	0.779	0.00000145	521
Missense in Polyphen		7	8.6492	0.80933		190
Synonymous	0.374	8	9.46	0.845	6.03e-7	139
Loss of Function	0.352	1	1.46	0.686	9.02e-8	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000367	0.0000367
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00116	0.000722
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Mineral absorption - Homo sapiens (human);Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.182

Intolerance Scores

• loftool: 0.393
• rvis_EVS: 0.15
• rvis_percentile_EVS: 63.81

Haploinsufficiency Scores

• pHI: 0.259
• hipred: N
• hipred_score: 0.215
• ghis: 0.401

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100g
• Phenotype: homeostasis/metabolism phenotype; normal phenotype

Gene ontology

• Cellular component: basolateral plasma membrane;apical plasma membrane
• Molecular function: vitamin D binding;calcium ion binding;transition metal ion binding