R3HDM1

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

Basic information

Region (hg38): 2:135531455-135725270

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.

• not_specified (109 variants)
• not_provided (2 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. These statistics are base on transcript: NM_001378107.1. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			105	5		110
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	105	6	0

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