S100PBP

protein-coding

S100P binding protein

Gene summary

This gene encodes a protein that was originally identified by its interaction with S100 calcium-binding protein P. Expression of this protein has been reported to be associated with pancreatic ductal adenocarcinoma. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2012]

MANE transcript

NM_022753.4

Inheritance

—

ClinVar variants

U:63B:9

Top phenotype

Charcot-Marie-Tooth disease dominant intermediate C

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr1:32,816,767-32,858,875

External References & Databases

Ensembl (ENSG00000116497)

Transcript & Mutation Effects

hg38 • Region Span ~42.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to S100PBP variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 69

Charcot-Marie-Tooth disease dominant intermediate CTotal: 7

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_022753.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			61 clinvar	8 clinvar		69
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	63	9	0	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 87 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_022753.4	RefSeq	NP_073590.2	5	MANE Select
ENST00000373475.10	Ensembl	ENSP00000362574.5	5	MANE Select
NM_001256121.2	RefSeq	NP_001243050.1	5	Standard
ENST00000373476.5	Ensembl	ENSP00000362575.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

calcium-dependent protein binding

Cellular Component

nucleus
cytosol
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373475
Coding exons: 5
Length: 42109
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125736
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0765	220	223	0.986	0.0000117	2672
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000038	0.000035	rare
South Asian	0.00021	0.00016	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.178
RVIS EVS: -0.29
RVIS percentile EVS: 33.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.865

Gene Damage Prediction

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