SPRR1A

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

Basic information

Region (hg38): 1:152984081-152985814

Links

ENSG00000169474 ∙ NCBI:6698 ∙ OMIM:182265 ∙ HGNC:11259 ∙ Uniprot:P35321 ∙ 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 SPRR1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRR1A 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			6	1		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	6	2	0

Variants in SPRR1A

This is a list of pathogenic ClinVar variants found in the SPRR1A region.

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

Position	Type	Phenotype	Significance	ClinVar
1-152985297-C-G		not specified	Uncertain significance (Mar 08, 2025)
1-152985300-C-A		not specified	Uncertain significance (Jan 10, 2023)
1-152985320-G-T		not specified	Uncertain significance (Jun 02, 2023)
1-152985352-G-A		not specified	Uncertain significance (Mar 01, 2024)
1-152985420-C-A		not specified	Uncertain significance (Apr 04, 2023)
1-152985428-G-A			Likely benign (Oct 01, 2024)
1-152985447-T-C		not specified	Uncertain significance (Oct 19, 2024)
1-152985457-C-A		not specified	Likely benign (May 30, 2024)
1-152985457-C-T		not specified	Uncertain significance (Dec 14, 2024)
1-152985486-A-T		not specified	Uncertain significance (Oct 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRR1A	protein_coding	protein_coding	ENST00000307122	1	1733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00604	0.514	125724	0	21	125745	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.693	59	45.8	1.29	0.00000205	565
Missense in Polyphen		21	17.794	1.1802		200
Synonymous	-0.342	20	18.1	1.10	8.71e-7	171
Loss of Function	-0.0565	3	2.90	1.04	1.25e-7	29

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000309	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
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.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.570
• rvis_EVS: 0.24
• rvis_percentile_EVS: 68.72

Haploinsufficiency Scores

• pHI: 0.0915
• hipred: N
• hipred_score: 0.112
• ghis: 0.389

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sprr1a

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;structural constituent of epidermis;protein binding, bridging