HID1

HID1 domain containing

Basic information

Region (hg38): 17:74950742-74973166

Previous symbols: [ "C17orf28" ]

Links

ENSG00000167861 ∙ NCBI:283987 ∙ OMIM:605752 ∙ HGNC:15736 ∙ Uniprot:Q8IV36 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• developmental and epileptic encephalopathy 105 with hypopituitarism (Strong), mode of inheritance: AR
• developmental and epileptic encephalopathy 105 with hypopituitarism (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Developmental and epileptic encephalopathy 105 with hypopituitarism	AR	Endocrine	Among other features, the condition can include hypopituitarism (eg, including central hypothyroidism), and awareness may allow early early identification and management of endocrine issues	Craniofacial; Endocrine; Genitourinary; Neurologic	33999436

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HID1 gene.

• not provided (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HID1 gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			62	1	2	65
nonsense		1				1
start loss						0
frameshift	2					2
inframe indel						0
splice donor/acceptor (+/-2bp)		1				1
splice region					2	2
non coding						0
Total	2	2	62	3	2

Variants in HID1

This is a list of pathogenic ClinVar variants found in the HID1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-74951577-C-T			Likely benign (Apr 01, 2023)
17-74951618-A-AG		Developmental and epileptic encephalopathy 105 with hypopituitarism	Pathogenic (Aug 12, 2022)
17-74951630-A-T		not specified	Uncertain significance (Aug 04, 2023)
17-74951934-GC-G		Developmental and epileptic encephalopathy 105 with hypopituitarism	Uncertain significance (Jun 15, 2023)
17-74951941-C-A		not specified	Uncertain significance (Sep 16, 2021)
17-74952035-G-A		not specified	Uncertain significance (Jun 09, 2022)
17-74952051-A-C		Developmental and epileptic encephalopathy 105 with hypopituitarism	Uncertain significance (Mar 29, 2024)
17-74952321-T-C		not specified	Uncertain significance (Jan 16, 2024)
17-74952357-G-C		not specified	Uncertain significance (Jan 23, 2023)
17-74952360-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-74953016-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-74953017-T-C		not specified	Uncertain significance (Mar 14, 2025)
17-74953026-A-G		not specified	Uncertain significance (Jan 19, 2025)
17-74953056-G-A		Inborn genetic diseases	Likely pathogenic (Oct 11, 2017)
17-74953071-A-G		not specified	Uncertain significance (Dec 19, 2022)
17-74953077-G-T		not specified	Uncertain significance (Feb 22, 2023)
17-74953079-C-A		not specified	Uncertain significance (Jun 10, 2022)
17-74953624-T-G		not specified	Uncertain significance (Apr 25, 2023)
17-74954170-C-T		not specified	Uncertain significance (Dec 07, 2024)
17-74954194-C-A		not specified	Uncertain significance (Nov 06, 2023)
17-74954194-C-T		not specified	Uncertain significance (May 03, 2023)
17-74954230-G-T		not specified	Uncertain significance (Dec 08, 2023)
17-74954236-G-C		not specified	Uncertain significance (Aug 28, 2023)
17-74954254-C-T		not specified	Uncertain significance (Jun 29, 2023)
17-74954255-G-A		not specified	Uncertain significance (Mar 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HID1	protein_coding	protein_coding	ENST00000425042	19	22424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0268	0.973	125705	0	21	125726	0.0000835

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.27	325	462	0.703	0.0000284	5065
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000122	0.000122
Ashkenazi Jewish	0.000516	0.000496
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000827	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000341	0.0000327
Other	0.000365	0.000326

dbNSFP

Source: dbNSFP

• 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

Haploinsufficiency Scores

• pHI: 0.158
• hipred: Y
• hipred_score: 0.614
• ghis: 0.563

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Hid1

Gene ontology

• Biological process: intracellular protein transport;response to brefeldin A
• Cellular component: Golgi trans cisterna;cytoplasm;Golgi apparatus;Golgi medial cisterna;cytosol;cytoplasmic microtubule;membrane;extracellular exosome;extrinsic component of Golgi membrane
• Molecular function: protein binding