S100A4

S100 calcium binding protein A4, the group of S100 calcium binding proteins|EF-hand domain containing

Basic information

Region (hg38): 1:153543612-153550136

Previous symbols: [ "MTS1", "CAPL" ]

Links

ENSG00000196154 ∙ NCBI:6275 ∙ OMIM:114210 ∙ HGNC:10494 ∙ Uniprot:P26447 ∙ 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 S100A4 gene.

• not provided (4 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100A4 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					4	4
missense			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	4

Variants in S100A4

This is a list of pathogenic ClinVar variants found in the S100A4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153543831-G-A			Benign (Dec 31, 2019)
1-153543860-C-T		not specified	Uncertain significance (Oct 12, 2021)
1-153543861-G-A			Benign (Mar 02, 2018)
1-153543882-G-A			Benign (Dec 31, 2019)
1-153544656-C-T		not specified	Uncertain significance (Jan 03, 2022)
1-153544735-C-T			Benign (Dec 31, 2019)
1-153547699-G-A		not specified	Uncertain significance (Sep 29, 2023)
1-153547710-C-A		not specified	Uncertain significance (Dec 19, 2023)
1-153547718-G-C		not specified	Uncertain significance (Jun 29, 2022)
1-153547759-G-A			Benign (Apr 04, 2024)
1-153547804-G-C			Likely benign (Mar 01, 2024)
1-153547821-T-C		not specified	Uncertain significance (Mar 01, 2024)
1-153547833-T-C		not specified	Uncertain significance (Mar 08, 2024)
1-153547845-G-C		not specified	Uncertain significance (Jan 10, 2022)
1-153548428-C-T		not specified	Uncertain significance (Nov 09, 2023)
1-153548449-C-A		not specified	Uncertain significance (Jun 29, 2022)
1-153548461-C-A		Malignant tumor of prostate	Uncertain significance (-)
1-153548463-G-A		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100A4	protein_coding	protein_coding	ENST00000368716	2	6524

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00618	0.519	125706	0	41	125747	0.000163

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.365	48	55.7	0.862	0.00000288	682
Missense in Polyphen		13	15.532	0.837		215
Synonymous	0.699	19	23.3	0.816	0.00000137	171
Loss of Function	-0.0357	3	2.93	1.02	1.22e-7	43

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000255	0.000255
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Vitamin D Receptor Pathway (Consensus)

Recessive Scores

• pRec: 0.520

Intolerance Scores

• loftool: 0.817
• rvis_EVS: -0.19
• rvis_percentile_EVS: 39.68

Haploinsufficiency Scores

• pHI: 0.262
• hipred: Y
• hipred_score: 0.778
• ghis: 0.610

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.815

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100a4
• Phenotype: immune system phenotype; cellular phenotype; neoplasm; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype

Gene ontology

• Biological process: epithelial to mesenchymal transition;positive regulation of I-kappaB kinase/NF-kappaB signaling
• Cellular component: extracellular region;extracellular space;nucleus;neuron projection;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: RNA binding;actin binding;calcium ion binding;protein binding;identical protein binding;transition metal ion binding;calcium-dependent protein binding;RAGE receptor binding