R3HDM1

R3H domain containing 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 2:135531454-135725270

Previous symbols: [ "R3HDM" ]

Links

ENSG00000048991 ∙ NCBI:23518 ∙ OMIM:619474 ∙ HGNC:9757 ∙ Uniprot:Q15032 ∙ 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 R3HDM1 gene.

• Inborn genetic diseases (37 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HDM1 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			36	1		37
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	1	0

Variants in R3HDM1

This is a list of pathogenic ClinVar variants found in the R3HDM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-135604931-T-C		not specified	Uncertain significance (Mar 13, 2023)
2-135616741-T-G		not specified	Uncertain significance (Dec 20, 2023)
2-135621576-G-A		not specified	Uncertain significance (Oct 26, 2022)
2-135635916-T-C		not specified	Uncertain significance (Oct 12, 2022)
2-135638749-G-A		not specified	Uncertain significance (Mar 22, 2022)
2-135638943-G-A		not specified	Uncertain significance (May 09, 2022)
2-135638962-G-T		not specified	Uncertain significance (Dec 19, 2023)
2-135641560-G-C		not specified	Uncertain significance (Feb 08, 2023)
2-135641568-A-G		not specified	Uncertain significance (Jan 27, 2022)
2-135641610-G-C		not specified	Uncertain significance (Jun 10, 2022)
2-135641647-A-G		not specified	Uncertain significance (May 18, 2023)
2-135641682-G-C		not specified	Uncertain significance (Nov 12, 2021)
2-135641724-T-C		not specified	Uncertain significance (Feb 22, 2023)
2-135641736-C-T		not specified	Uncertain significance (Jun 07, 2023)
2-135641746-C-T		not specified	Uncertain significance (Dec 06, 2023)
2-135645430-T-C		not specified	Uncertain significance (Mar 01, 2023)
2-135645442-C-G		not specified	Uncertain significance (Jan 23, 2024)
2-135651791-G-A		not specified	Uncertain significance (May 03, 2023)
2-135651806-C-G		not specified	Uncertain significance (Jun 24, 2022)
2-135651851-C-G		not specified	Uncertain significance (Dec 19, 2022)
2-135651865-A-G		not specified	Uncertain significance (Jul 09, 2021)
2-135651875-C-T		not specified	Uncertain significance (May 23, 2023)
2-135651884-A-G		not specified	Uncertain significance (Jan 26, 2022)
2-135651889-C-G		not specified	Uncertain significance (Jan 10, 2023)
2-135651889-C-T		not specified	Uncertain significance (Dec 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
R3HDM1	protein_coding	protein_coding	ENST00000264160	24	193816

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.861	0.139	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.85	463	589	0.786	0.0000297	7196
Missense in Polyphen		95	166.78	0.56961		2127
Synonymous	-1.14	225	204	1.10	0.0000102	2125
Loss of Function	5.69	12	59.3	0.202	0.00000294	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.000101	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000726	0.0000703
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0753

Intolerance Scores

• loftool: 0.594
• rvis_EVS: -0.09
• rvis_percentile_EVS: 47.12

Haploinsufficiency Scores

• pHI: 0.500
• hipred: N
• hipred_score: 0.492
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.415

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: R3hdm1
• Phenotype: reproductive system phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Molecular function: RNA binding