SPRR1B

small proline rich protein 1B, the group of Small proline rich proteins

Basic information

Region (hg38): 1:153031203-153032900

Previous symbols: [ "SPRR1" ]

Links

ENSG00000169469 ∙ NCBI:6699 ∙ OMIM:182266 ∙ HGNC:11260 ∙ Uniprot:P22528 ∙ 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 SPRR1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRR1B 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	0	0

Variants in SPRR1B

This is a list of pathogenic ClinVar variants found in the SPRR1B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153032391-C-A		not specified	Uncertain significance (Oct 05, 2023)
1-153032397-C-A		not specified	Uncertain significance (Apr 19, 2023)
1-153032413-A-G		not specified	Uncertain significance (Sep 26, 2024)
1-153032439-C-A		not specified	Uncertain significance (Oct 27, 2023)
1-153032442-T-G		not specified	Uncertain significance (Jun 10, 2024)
1-153032471-C-A		not specified	Uncertain significance (Dec 23, 2024)
1-153032472-C-T		not specified	Uncertain significance (Nov 09, 2024)
1-153032526-G-A		not specified	Uncertain significance (Aug 12, 2024)
1-153032526-G-C		not specified	Uncertain significance (Apr 26, 2023)
1-153032543-C-G		not specified	Uncertain significance (Aug 19, 2023)
1-153032545-C-G		not specified	Uncertain significance (Aug 26, 2024)
1-153032565-C-T		not specified	Uncertain significance (Feb 08, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRR1B	protein_coding	protein_coding	ENST00000307098	1	1699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000632	0.305	125736	0	7	125743	0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.637	58	45.9	1.26	0.00000204	575
Missense in Polyphen		15	14.413	1.0407		175
Synonymous	-0.569	20	17.0	1.18	7.49e-7	169
Loss of Function	-0.755	4	2.67	1.50	1.18e-7	27

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000995	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cross-linked envelope protein of keratinocytes. It is a keratinocyte protein that first appears in the cell cytosol, but ultimately becomes cross-linked to membrane proteins by transglutaminase. All that results in the formation of an insoluble envelope beneath the plasma membrane. Can function as both amine donor and acceptor in transglutaminase-mediated cross- linkage.
• Pathway: Vitamin D Receptor Pathway;Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.450
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.28

Haploinsufficiency Scores

• pHI: 0.0820
• hipred: N
• hipred_score: 0.168
• ghis: 0.427

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0702

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sprr1b
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Biological process: epidermis development;peptide cross-linking;keratinocyte differentiation;cornification
• Cellular component: cornified envelope;cytoplasm;cytosol
• Molecular function: structural molecule activity;protein binding, bridging