R3HDM2

R3H domain containing 2

Basic information

Region (hg38): 12:57253762-57431043

Links

ENSG00000179912NCBI:22864OMIM:619886HGNC:29167Uniprot:Q9Y2K5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the R3HDM2 gene.

  • not_specified (94 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HDM2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001394031.1. 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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
missense
91
clinvar
91
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 91 0 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
R3HDM2protein_codingprotein_codingENST00000347140 22181397
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.00000484125743031257460.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.333215380.5970.00002886422
Missense in Polyphen58147.570.393042009
Synonymous2.331551970.7880.00001021881
Loss of Function6.16451.90.07710.00000253575

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00003410.0000341
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000008870.00000879
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.108

Intolerance Scores

loftool
0.0829
rvis_EVS
-0.6
rvis_percentile_EVS
18.06

Haploinsufficiency Scores

pHI
0.387
hipred
Y
hipred_score
0.631
ghis
0.579

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.773

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
R3hdm2
Phenotype

Gene ontology

Biological process
Cellular component
nucleus
Molecular function
RNA binding