S100A5

S100 calcium binding protein A5, the group of EF-hand domain containing|S100 calcium binding proteins

Basic information

Region (hg38): 1:153537147-153541765

Previous symbols: [ "S100D" ]

Links

ENSG00000196420 ∙ NCBI:6276 ∙ OMIM:176991 ∙ HGNC:10495 ∙ Uniprot:P33763 ∙ 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 S100A5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A5 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in S100A5

This is a list of pathogenic ClinVar variants found in the S100A5 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153537324-T-C		not specified	Uncertain significance (Sep 30, 2021)
1-153537341-C-A		not specified	Uncertain significance (May 01, 2024)
1-153537384-T-A		not specified	Uncertain significance (Mar 16, 2022)
1-153537385-C-T		not specified	Uncertain significance (Mar 23, 2022)
1-153537419-G-C		not specified	Uncertain significance (Jan 05, 2022)
1-153537425-G-C		not specified	Uncertain significance (Oct 02, 2023)
1-153540101-T-A		not specified	Uncertain significance (Jan 09, 2024)
1-153540119-T-C		not specified	Uncertain significance (May 13, 2022)
1-153540133-G-A		not specified	Uncertain significance (Jan 30, 2024)
1-153540157-A-G		not specified	Uncertain significance (Sep 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A5	protein_coding	protein_coding	ENST00000368718	2	4619

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000551	0.151	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.132	54	51.3	1.05	0.00000266	620
Missense in Polyphen		16	17.641	0.90698		211
Synonymous	-0.646	27	23.1	1.17	0.00000152	157
Loss of Function	-1.53	5	2.43	2.06	9.96e-8	40

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000264	0.0000264
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds calcium, zinc and copper. One subunit can simultaneously bind 2 calcium ions or 2 copper ions plus 1 zinc ion. Calcium and copper ions compete for the same binding sites. {ECO:0000269|PubMed:10882717}.

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.662
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.0650
• hipred: N
• hipred_score: 0.170
• ghis: 0.398

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• gene_indispensability_pred: N
• gene_indispensability_score: 0.150

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a5
• Phenotype: taste/olfaction phenotype; normal phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Cellular component: nucleus;neuronal cell body
• Molecular function: copper ion binding;calcium ion binding;zinc ion binding;protein homodimerization activity