SPRR2D

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

Basic information

Region (hg38): 1:153039732-153041931

Links

ENSG00000163216 ∙ NCBI:6703 ∙ OMIM:617587 ∙ HGNC:11264 ∙ Uniprot:P22532 ∙ 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 SPRR2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPRR2D 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			8	1		9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	1	0

Variants in SPRR2D

This is a list of pathogenic ClinVar variants found in the SPRR2D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153040144-G-T		not specified	Uncertain significance (Mar 05, 2025)
1-153040165-G-A		not specified	Uncertain significance (Apr 22, 2022)
1-153040177-A-C		not specified	Uncertain significance (Jul 14, 2021)
1-153040201-T-C		not specified	Uncertain significance (Mar 18, 2024)
1-153040208-G-T		not specified	Uncertain significance (Oct 27, 2021)
1-153040226-A-G		not specified	Uncertain significance (Jul 31, 2024)
1-153040235-A-G		not specified	Likely benign (Aug 16, 2021)
1-153040250-G-A		not specified	Uncertain significance (Jul 30, 2024)
1-153040258-G-A		not specified	Uncertain significance (Aug 26, 2024)
1-153040264-G-A		not specified	Uncertain significance (Jan 08, 2024)
1-153040301-G-A		not specified	Uncertain significance (Jan 09, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPRR2D	protein_coding	protein_coding	ENST00000368757	1	2207

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0159	0.481	124518	0	37	124555	0.000149

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.681	51	39.0	1.31	0.00000185	457
Missense in Polyphen
Synonymous	-2.26	27	15.6	1.73	8.24e-7	139
Loss of Function	-0.617	2	1.25	1.59	5.45e-8	11

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000752	0.000752
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000445	0.0000444
Middle Eastern	0.000272	0.000272
South Asian	0.00	0.00
Other	0.000164	0.000164

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)

Intolerance Scores

• loftool: 0.748
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.57

Haploinsufficiency Scores

• pHI: 0.0965
• hipred: N
• hipred_score: 0.112
• ghis: 0.398

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