S100PBP

S100P binding protein

Basic information

Region (hg38): 1:32816767-32858875

Links

ENSG00000116497 ∙ NCBI:64766 ∙ OMIM:611889 ∙ HGNC:25768 ∙ Uniprot:Q96BU1 ∙ 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 S100PBP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the S100PBP 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				1		1
missense			29	5		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4	1	8	13
Total	0	0	33	7	8

Variants in S100PBP

This is a list of pathogenic ClinVar variants found in the S100PBP region.

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

Position	Type	Phenotype	Significance	ClinVar
1-32816919-G-C			Likely benign (Nov 08, 2018)
1-32817014-G-A			Benign (Aug 30, 2018)
1-32817172-A-G		not specified • Charcot-Marie-Tooth disease dominant intermediate C	Likely benign (Oct 10, 2024)
1-32817174-C-A		Charcot-Marie-Tooth disease dominant intermediate C • not specified	Benign (Feb 03, 2025)
1-32817178-C-A		Charcot-Marie-Tooth disease dominant intermediate C	Likely benign (Sep 06, 2023)
1-32817178-C-T		Charcot-Marie-Tooth disease dominant intermediate C	Likely benign (Feb 02, 2021)
1-32817184-T-A		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (May 16, 2021)
1-32817187-C-A		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Aug 24, 2023)
1-32817187-C-T		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Oct 03, 2021)
1-32817190-G-T		Inborn genetic diseases	Uncertain significance (Mar 31, 2023)
1-32817191-C-A		Charcot-Marie-Tooth disease dominant intermediate C	Likely benign (Aug 24, 2023)
1-32817193-G-A		not specified • Charcot-Marie-Tooth disease dominant intermediate C • Inborn genetic diseases	Benign/Likely benign (Jan 31, 2025)
1-32817198-C-T		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Jun 13, 2024)
1-32817199-G-A		Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset	Likely pathogenic (-)
1-32817200-G-A		Charcot-Marie-Tooth disease dominant intermediate C	Conflicting classifications of pathogenicity (Oct 13, 2024)
1-32817201-G-T		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Dec 22, 2020)
1-32817202-T-C		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Apr 06, 2023)
1-32817203-G-A		Charcot-Marie-Tooth disease dominant intermediate C	Likely benign (Dec 23, 2021)
1-32817204-A-G		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Feb 14, 2023)
1-32817205-T-A		Charcot-Marie-Tooth disease dominant intermediate C • Inborn genetic diseases • not specified	Conflicting classifications of pathogenicity (Mar 19, 2025)
1-32817228-C-T		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Feb 07, 2024)
1-32817236-G-GT			Uncertain significance (Mar 19, 2023)
1-32817272-C-T		not specified	Likely benign (Jan 05, 2017)
1-32817354-C-T		Charcot-Marie-Tooth disease dominant intermediate C	Uncertain significance (Jan 12, 2018)
1-32817373-G-T		Charcot-Marie-Tooth disease dominant intermediate C	Benign (Jan 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
S100PBP	protein_coding	protein_coding	ENST00000373475	5	42109

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.945	0.0549	125726	0	10	125736	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0765	220	223	0.986	0.0000117	2672
Missense in Polyphen		51	63.364	0.80487		847
Synonymous	-0.840	95	85.1	1.12	0.00000460	791
Loss of Function	3.49	2	18.0	0.111	0.00000101	209

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000376	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.000206	0.000163
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.178
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.2

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.273
• ghis: 0.604

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.865

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: S100pbp

Gene ontology

• Cellular component: nucleus;cytosol;nuclear speck
• Molecular function: calcium-dependent protein binding