RPTN

repetin, the group of EF-hand domain containing|S100 fused type protein family

Basic information

Region (hg38): 1:152153595-152159228

Links

ENSG00000215853 ∙ NCBI:126638 ∙ OMIM:613259 ∙ HGNC:26809 ∙ Uniprot:Q6XPR3 ∙ 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 RPTN gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RPTN 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		2
missense			52	10		62
nonsense						0
start loss						0
frameshift						0
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	12	1

Variants in RPTN

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

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

Position	Type	Phenotype	Significance	ClinVar
1-152154808-T-A		not specified	Uncertain significance (Jan 05, 2022)
1-152154841-C-T		not specified	Likely benign (Apr 13, 2023)
1-152154850-T-C		not specified	Uncertain significance (May 10, 2022)
1-152154896-T-C		not specified	Likely benign (Feb 13, 2023)
1-152154904-C-T		not specified	Likely benign (Jul 25, 2023)
1-152154908-T-C		not specified	Uncertain significance (May 20, 2024)
1-152154926-G-C		not specified	Uncertain significance (Feb 10, 2025)
1-152154932-C-T		not specified	Uncertain significance (Dec 06, 2022)
1-152154941-C-T		not specified	Uncertain significance (Dec 01, 2022)
1-152154950-G-A		not specified	Uncertain significance (Mar 31, 2023)
1-152154961-G-C		not specified	Likely benign (Jul 14, 2024)
1-152154986-C-T		not specified	Uncertain significance (Jan 23, 2025)
1-152154989-A-G		not specified	Uncertain significance (Jul 26, 2022)
1-152155157-C-G		not specified	Uncertain significance (Apr 23, 2024)
1-152155166-C-T		not specified	Likely benign (Aug 23, 2021)
1-152155202-C-T		not specified	Uncertain significance (Apr 25, 2023)
1-152155216-C-A		not specified	Likely benign (Dec 23, 2024)
1-152155231-G-A		not specified	Uncertain significance (Aug 30, 2022)
1-152155262-A-G		not specified	Uncertain significance (Nov 06, 2023)
1-152155328-T-A		not specified	Uncertain significance (Oct 25, 2024)
1-152155349-T-G		not specified	Uncertain significance (Sep 18, 2024)
1-152155354-T-C		not specified	Uncertain significance (Sep 01, 2021)
1-152155378-G-C		not specified	Uncertain significance (Aug 08, 2024)
1-152155420-C-T		not specified	Uncertain significance (Aug 05, 2024)
1-152155462-T-C		not specified	Uncertain significance (Jun 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RPTN	protein_coding	protein_coding	ENST00000316073	2	5634

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000255	0.772	124238	4	358	124600	0.00145

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.481	400	374	1.07	0.0000186	5274
Missense in Polyphen		47	56.296	0.83487		915
Synonymous	-1.10	156	139	1.12	0.00000724	1300
Loss of Function	1.17	9	13.6	0.660	6.11e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000521	0.000521
Ashkenazi Jewish	0.00	0.00
East Asian	0.00367	0.00368
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000381	0.000381
Middle Eastern	0.00367	0.00368
South Asian	0.00765	0.00754
Other	0.000660	0.000659

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the cornified cell envelope formation. Multifunctional epidermal matrix protein. Reversibly binds calcium.
• Pathway: Keratinization;Developmental Biology;Formation of the cornified envelope (Consensus)

Intolerance Scores

• loftool: 0.956
• rvis_EVS: 1.24
• rvis_percentile_EVS: 93.42

Haploinsufficiency Scores

• pHI: 0.0961
• hipred: N
• hipred_score: 0.112
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.357

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rptn

Gene ontology

• Biological process: cornification
• Cellular component: cornified envelope;extracellular region;cytosol
• Molecular function: calcium ion binding;transition metal ion binding