RHD
Rh blood group D antigen, the group of CD molecules|Blood group antigens
Basic information
Region (hg38): 1:25272392-25330445
Previous symbols: [ "RH" ]
Links
Phenotypes
GenCC
Source:
- Rh deficiency syndrome (Supportive), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Rhesus blood group | BG | Hematologic | Variants associated with a blood group may be important in specific situations (eg, related to transfusion) | Hematologic | 8808597; 9845715; 986418; 10504121; 21277262 |
ClinVar
This is a list of variants' phenotypes submitted to
- - (11 variants)
- not provided (4 variants)
- Inborn genetic diseases (4 variants)
- weakened D expression by serology (3 variants)
- RhD negative (1 variants)
- RhD category D-VII (1 variants)
- Rhd, weak d, type I (1 variants)
- Hemolytic disease of fetus OR newborn due to RhD isoimmunization (1 variants)
- Weakened expression of D antigen (1 variants)
- Anti-D isoimmunization affecting pregnancy (1 variants)
- Blood group antigen abnormality (1 variants)
- serologic weak D phenotype (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RHD gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 2 | 3 | |||
| missense | 2 | 3 | 1 | 6 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 1 | 1 | ||||
| Total | 2 | 0 | 3 | 2 | 3 |
Highest pathogenic variant AF is 0.00251
Variants in RHD
This is a list of pathogenic ClinVar variants found in the RHD region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-25284610-G-T | - | no interpretation for the single variant (-) | ||
| 1-25284678-C-T | Likely benign (Nov 01, 2022) | |||
| 1-25284694-G-C | Weakened expression of D antigen | Affects (Jan 14, 2019) | ||
| 1-25284701-CT-GG | weakened D expression by serology | Affects (Jul 01, 2021) | ||
| 1-25284753-T-C | RhD category D-VII | Pathogenic (May 01, 1995) | ||
| 1-25290646-G-C | weakened D expression by serology | Affects (-) | ||
| 1-25290671-G-A | Likely benign (Apr 09, 2018) | |||
| 1-25290715-C-T | - | no interpretation for the single variant (-) | ||
| 1-25290757-G-A | Blood group antigen abnormality | Affects (Mar 03, 2016) | ||
| 1-25290760-A-C | - | no interpretation for the single variant (-) | ||
| 1-25290800-T-C | Benign (Aug 16, 2018) | |||
| 1-25300968-T-C | - | no interpretation for the single variant (-) | ||
| 1-25301000-C-G | Inborn genetic diseases | Uncertain significance (May 01, 2022) | ||
| 1-25301061-C-G | - | no interpretation for the single variant (-) | ||
| 1-25301063-G-A | - | no interpretation for the single variant (-) | ||
| 1-25301068-G-A | Benign (Jul 16, 2018) | |||
| 1-25301070-T-A | serologic weak D phenotype | Affects (Sep 04, 2020) | ||
| 1-25301552-T-G | - | no interpretation for the single variant (-) | ||
| 1-25301556-A-C | Inborn genetic diseases | Uncertain significance (Oct 26, 2022) | ||
| 1-25301582-G-C | - | no interpretation for the single variant (-) | ||
| 1-25301594-G-A | weakened D expression by serology | Affects (Jul 01, 2021) | ||
| 1-25301618-G-C | - | no interpretation for the single variant (-) | ||
| 1-25301629-C-T | Benign/Likely benign (Jul 01, 2023) | |||
| 1-25301670-A-G | Inborn genetic diseases | Likely benign (Jul 13, 2022) | ||
| 1-25301680-C-G | Inborn genetic diseases | Uncertain significance (Dec 28, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RHD | protein_coding | protein_coding | ENST00000328664 | 10 | 58053 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0000285 | 0.937 | 112308 | 140 | 514 | 112962 | 0.00290 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.326 | 226 | 213 | 1.06 | 0.0000125 | 2666 |
| Missense in Polyphen | 71 | 69.28 | 1.0248 | 994 | ||
| Synonymous | -0.489 | 97 | 91.1 | 1.07 | 0.00000620 | 857 |
| Loss of Function | 1.72 | 10 | 17.8 | 0.561 | 9.56e-7 | 208 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0459 | 0.0379 |
| Ashkenazi Jewish | 0.000871 | 0.000762 |
| East Asian | 0.000381 | 0.000327 |
| Finnish | 0.000105 | 0.0000522 |
| European (Non-Finnish) | 0.000158 | 0.000125 |
| Middle Eastern | 0.000381 | 0.000327 |
| South Asian | 0.000419 | 0.000314 |
| Other | 0.00112 | 0.000913 |
dbNSFP
Source:
- Function
- FUNCTION: May be part of an oligomeric complex which is likely to have a transport or channel function in the erythrocyte membrane.;
Intolerance Scores
- loftool
- 0.938
- rvis_EVS
- 3.31
- rvis_percentile_EVS
- 99.42
Haploinsufficiency Scores
- pHI
- 0.404
- hipred
- N
- hipred_score
- 0.132
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.00250
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rhd
- Phenotype
- hematopoietic system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- ammonium transmembrane transport
- Cellular component
- integral component of plasma membrane
- Molecular function
- ammonium transmembrane transporter activity