SPRR2F

small proline rich protein 2F, the group of Small proline rich proteins

Basic information

Region (hg38): 1:153112121-153113516

Links

ENSG00000244094 ∙ NCBI:6705 ∙ OMIM:617589 ∙ HGNC:11266 ∙ Uniprot:Q96RM1 ∙ 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 SPRR2F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRR2F 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			4	2		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	2	0

Variants in SPRR2F

This is a list of pathogenic ClinVar variants found in the SPRR2F region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153112541-G-A		not specified	Uncertain significance (Jul 20, 2021)
1-153112546-C-T		not specified	Uncertain significance (Mar 14, 2023)
1-153112579-T-A		not specified	Uncertain significance (Dec 16, 2023)
1-153112604-A-G		not specified	Likely benign (Aug 02, 2022)
1-153112619-A-G		not specified	Likely benign (Aug 02, 2022)
1-153112666-C-G		not specified	Uncertain significance (Aug 21, 2024)
1-153112705-T-G		not specified	Uncertain significance (Dec 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRR2F	protein_coding	protein_coding	ENST00000468739	1	1402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0852	0.573	125014	0	3	125017	0.0000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.173	41	38.0	1.08	0.00000171	454
Missense in Polyphen
Synonymous	-1.12	22	16.3	1.35	9.38e-7	137
Loss of Function	-0.136	1	0.863	1.16	3.72e-8	8

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000266
Middle Eastern	0.00	0.00
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 (By similarity). {ECO:0000250}.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Intolerance Scores

• loftool: 0.619
• rvis_EVS: 0.9
• rvis_percentile_EVS: 89.35

Haploinsufficiency Scores

• pHI: 0.101
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

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