R3HDML

R3H domain containing like, the group of CAP superfamily

Basic information

Region (hg38): 20:44337043-44351238

Links

ENSG00000101074 ∙ NCBI:140902 ∙ ∙ HGNC:16249 ∙ Uniprot:Q9H3Y0 ∙ 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 R3HDML gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HDML 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in R3HDML

This is a list of pathogenic ClinVar variants found in the R3HDML region.

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

Position	Type	Phenotype	Significance	ClinVar
20-44337179-G-A		not specified	Uncertain significance (Sep 20, 2023)
20-44337192-G-A		not specified	Uncertain significance (Jun 03, 2022)
20-44337237-C-T		not specified	Uncertain significance (Apr 08, 2024)
20-44337240-A-G		not specified	Uncertain significance (Jun 29, 2023)
20-44337248-C-A		not specified	Uncertain significance (Sep 29, 2023)
20-44337255-C-T		not specified	Likely benign (Dec 07, 2021)
20-44337308-A-G		not specified	Uncertain significance (Nov 06, 2023)
20-44337324-G-A		not specified	Uncertain significance (Oct 29, 2021)
20-44337363-A-T		not specified	Uncertain significance (Jun 07, 2023)
20-44337378-G-A		not specified	Uncertain significance (Feb 15, 2023)
20-44337380-G-A		not specified	Uncertain significance (Jun 05, 2024)
20-44341199-T-A		not specified	Uncertain significance (Sep 20, 2023)
20-44341221-C-A		not specified	Uncertain significance (Apr 07, 2022)
20-44341311-G-A		not specified	Uncertain significance (Sep 26, 2022)
20-44343474-C-T		not specified	Uncertain significance (Oct 13, 2023)
20-44343480-G-A		not specified	Uncertain significance (Jul 14, 2021)
20-44343499-A-G		not specified	Uncertain significance (Nov 18, 2022)
20-44343499-A-T		not specified	Uncertain significance (Mar 25, 2024)
20-44345266-G-A		not specified	Uncertain significance (Feb 15, 2023)
20-44345324-T-G		not specified	Uncertain significance (Jul 19, 2023)
20-44345371-G-A		not specified	Uncertain significance (Oct 05, 2023)
20-44350667-T-G		not specified	Uncertain significance (Mar 28, 2024)
20-44350676-G-A		not specified	Uncertain significance (Nov 12, 2021)
20-44350683-C-T		not specified	Uncertain significance (May 31, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
R3HDML	protein_coding	protein_coding	ENST00000217043	5	14250

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000188	0.458	125272	0	476	125748	0.00189

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.545	144	164	0.880	0.00000994	1658
Missense in Polyphen		38	45.844	0.82889		494
Synonymous	-0.475	71	66.1	1.07	0.00000421	486
Loss of Function	0.653	10	12.5	0.801	5.35e-7	129

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00260	0.00260
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00120	0.00120
European (Non-Finnish)	0.00317	0.00315
Middle Eastern	0.00	0.00
South Asian	0.000133	0.000131
Other	0.00213	0.00212

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative serine protease inhibitor. {ECO:0000250}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.759
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.63

Haploinsufficiency Scores

• pHI: 0.375
• hipred: N
• hipred_score: 0.342

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0803

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: R3hdml

Gene ontology

• Biological process: negative regulation of peptidase activity
• Cellular component: extracellular space
• Molecular function: peptidase inhibitor activity