SPRR3

small proline rich protein 3, the group of Small proline rich proteins

Basic information

Region (hg38): 1:153001747-153003856

Links

ENSG00000163209 ∙ NCBI:6707 ∙ OMIM:182271 ∙ HGNC:11268 ∙ Uniprot:Q9UBC9 ∙ 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 SPRR3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRR3 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				2	1	3
missense			14	1	2	17
nonsense						0
start loss						0
frameshift				1	1	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	4

Variants in SPRR3

This is a list of pathogenic ClinVar variants found in the SPRR3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153003045-A-C		not specified	Likely benign (Aug 28, 2024)
1-153003079-A-G		not specified	Uncertain significance (Jan 23, 2023)
1-153003086-A-C		not specified	Uncertain significance (Sep 14, 2022)
1-153003105-C-T		not specified	Uncertain significance (Aug 26, 2024)
1-153003114-A-C		not specified	Uncertain significance (Jun 16, 2023)
1-153003153-G-T		not specified	Uncertain significance (Dec 30, 2024)
1-153003184-A-G		not specified	Uncertain significance (Oct 27, 2021)
1-153003199-AGGTCCCT-A			Benign (Jul 19, 2018)
1-153003205-C-A		not specified	Uncertain significance (Dec 02, 2024)
1-153003208-AGCCAGGCTGTACCAAGG-A			Likely benign (Jul 19, 2018)
1-153003272-G-A			Benign (Apr 23, 2018)
1-153003276-C-T		not specified	Uncertain significance (Nov 09, 2024)
1-153003277-C-T		not specified	Uncertain significance (Mar 29, 2024)
1-153003287-C-T			Likely benign (Jan 01, 2025)
1-153003322-T-C		not specified	Uncertain significance (Apr 03, 2023)
1-153003324-C-A		not specified	Uncertain significance (Dec 04, 2024)
1-153003334-G-A			Benign (Jul 09, 2018)
1-153003387-A-C		not specified	Uncertain significance (Feb 09, 2022)
1-153003398-T-C			Likely benign (Jun 01, 2024)
1-153003436-C-T		not specified	Uncertain significance (Jun 24, 2022)
1-153003447-G-A		not specified	Uncertain significance (Aug 01, 2024)
1-153003460-C-G			Benign (May 21, 2018)
1-153003508-A-G		not specified	Uncertain significance (Mar 31, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRR3	protein_coding	protein_coding	ENST00000331860	1	2110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.148	80	83.8	0.954	0.00000378	1057
Missense in Polyphen		13	17.738	0.73287		227
Synonymous	0.574	27	31.1	0.869	0.00000146	343
Loss of Function

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cross-linked envelope protein of keratinocytes.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.0660

Intolerance Scores

• loftool: 0.984
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.46

Haploinsufficiency Scores

• pHI: 0.0206
• hipred: N
• hipred_score: 0.112
• ghis: 0.387

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00178

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sprr3
• Phenotype: cellular phenotype; muscle phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); normal phenotype; skeleton phenotype

Gene ontology

• Biological process: epidermis development;peptide cross-linking;keratinocyte differentiation;wound healing;cornification
• Cellular component: cornified envelope;cytoplasm;Golgi apparatus;cytosol;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: structural molecule activity;protein binding