SPRR4

small proline rich protein 4, the group of Small proline rich proteins

Basic information

Region (hg38): 1:152970648-152972574

Links

ENSG00000184148 ∙ NCBI:163778 ∙ OMIM:616363 ∙ HGNC:23173 ∙ Uniprot:Q96PI1 ∙ 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 SPRR4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRR4 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in SPRR4

This is a list of pathogenic ClinVar variants found in the SPRR4 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152971894-T-A		not specified	Uncertain significance (Jun 02, 2024)
1-152971970-G-C		not specified	Uncertain significance (Oct 26, 2024)
1-152971981-C-G		not specified	Uncertain significance (Aug 08, 2023)
1-152971990-T-G		not specified	Uncertain significance (May 09, 2023)
1-152972053-C-T		not specified	Uncertain significance (May 31, 2023)
1-152972063-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-152972083-C-G		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRR4	protein_coding	protein_coding	ENST00000328051	1	1909

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0389	0.660	125671	0	72	125743	0.000286

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.11	59	39.5	1.50	0.00000190	510
Missense in Polyphen
Synonymous	1.51	8	15.6	0.513	7.55e-7	142
Loss of Function	0.443	2	2.80	0.714	1.24e-7	25

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00721	0.00392
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cross-linked envelope protein of keratinocytes. Involved in UV-induced cornification.

Recessive Scores

• pRec: 0.0526

Intolerance Scores

• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.123
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0238

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sprr4

Gene ontology

• Biological process: peptide cross-linking;keratinocyte differentiation;keratinization
• Cellular component: cornified envelope;cytoplasm;cell cortex
• Molecular function: structural molecule activity