HIGD1B

protein-coding

HIG1 hypoxia inducible domain family member 1B

Gene summary

This gene encodes a member of the hypoxia inducible gene 1 (HIG1) domain family. The encoded protein is localized to the cell membrane and has been linked to tumorigenesis and the progression of pituitary adenomas. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2012]

MANE transcript

NM_016438.4

Inheritance

—

ClinVar variants

U:19B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.25

Max pathogenic AF

—

Genomic locus

chr17:44,846,353-44,850,476

External References & Databases

Ensembl (ENSG00000131097)

Transcript & Mutation Effects

hg38 • Region Span ~4.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HIGD1B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 20

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016438.4. 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						0
missense			19 clinvar	3 clinvar		22
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	19	3	0	22

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016438.4	RefSeq	NP_057522.1	3	MANE Select
ENST00000253410.3	Ensembl	ENSP00000253410.1	3	MANE Select
NM_001271880.2	RefSeq	NP_001258809.1	3	Standard
ENST00000586911.1	Ensembl	ENSP00000465657.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000253410
Coding exons: 3
Length: 4128
Individuals with no LoFs: 125691
Homozygous LoFs: 0
Heterozygous LoFs: 54
Defined: 125745
p: 0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.219	68	63.1	1.08	0.00000373	625
Missense (PolyPhen)		17	20.924	0.81246		209
Synonymous	-0.383	24	21.7	1.10	0.00000130	201
Loss of Function	-0.502	6	4.81	1.25	2.90e-7	47

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00026	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.00078	0.00078	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0751

Intolerance Scores

LoFtool: 0.688
RVIS EVS: 0.42
RVIS percentile EVS: 76.81

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.781

Gene Damage Prediction

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