R3HDM4

R3H domain containing 4

Basic information

Region (hg38): 19:896503-913245

Previous symbols: [ "C19orf22" ]

Links

ENSG00000198858NCBI:91300HGNC:28270Uniprot:Q96D70AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the R3HDM4 gene.

  • not_specified (48 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the R3HDM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000138774.4. 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
0
missense
47
clinvar
1
clinvar
48
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 47 1 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
R3HDM4protein_codingprotein_codingENST00000361574 816738
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0004630.8801255651311255970.000127
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5321771581.120.00001121679
Missense in Polyphen6668.9240.95757632
Synonymous-1.368267.81.210.00000442566
Loss of Function1.38712.20.5735.97e-7155

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001550.000154
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0002390.000231
European (Non-Finnish)0.0001780.000159
Middle Eastern0.00005440.0000544
South Asian0.0001010.0000980
Other0.0001710.000163

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.109

Intolerance Scores

loftool
rvis_EVS
0.26
rvis_percentile_EVS
70.44

Haploinsufficiency Scores

pHI
0.146
hipred
N
hipred_score
0.325
ghis
0.529

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.114

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
R3hdm4
Phenotype

Gene ontology

Biological process
Cellular component
nucleus
Molecular function
nucleic acid binding