HID1
protein-codingHID1 domain containing
Gene summary
Predicted to act upstream of or within several processes, including insulin processing; secretory granule maturation; and vacuole fusion, non-autophagic. Located in Golgi apparatus; cytoplasmic microtubule; and cytosol. Implicated in developmental and epileptic encephalopathy 105. [provided by Alliance of Genome Resources, Jul 2025]
- C17orf28
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~22.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0031028
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0031028
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0031028
Submitter: Ambry Genetics
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Endocrine; Genitourinary; Neurologic
Intervention: Endocrine
Rationale: Among other features, the condition can include hypopituitarism (eg, including central hypothyroidism), and awareness may allow early early identification and management of endocrine issues
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to HID1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_030630.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 5 | 1 | 9 | ||
| missense | 2 | 125 | 1 | 2 | 130 | |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 4 | 2 | 1 | 7 | ||
| splice donor/acceptor (+/-2bp) | 2 | 2 | 4 | |||
| Total | 6 | 5 | 131 | 6 | 3 | 151 |
Highest pathogenic variant AF is 0.000018544797
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_085133.1 | 19 | MANE Select | |
| Ensembl | ENSP00000413520.2 | 19 | MANE Select | |
| Ensembl | ENSP00000317795.7 | 6 | Standard | |
| Ensembl | ENSP00000431131.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- intracellular protein transport
- response to brefeldin A
Molecular Function
- protein binding
Cellular Component
- Golgi trans cisterna
- cytoplasm
- Golgi apparatus
- Golgi medial cisterna
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000425042
- Coding exons
- 19
- Length
- 22424
- Individuals with no LoFs
- 125705
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 21
- Defined
- 125726
- p
- 0.0000835
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.27 | 325 | 462 | 0.703 | 0.0000284 | 5065 |
| Missense (PolyPhen) | 82 | 157.46 | 0.52078 | 1782 | ||
| Synonymous | 0.631 | 185 | 196 | 0.943 | 0.0000120 | 1584 |
| Loss of Function | 4.02 | 10 | 36.0 | 0.277 | 0.00000170 | 413 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0.00052 | 0.00050 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000083 | 0.000079 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0.00036 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play an important role in the development of cancers in a broad range of tissues. {ECO:0000269|PubMed:11281419}.;
Recessive Scores
- pRec
- 0.0996
Intolerance Scores
- RVIS EVS
- -1.17
- RVIS percentile EVS
- 6.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |