HIGD1B

HIG1 hypoxia inducible domain family member 1B

Basic information

Region (hg38): 17:44846353-44850476

Links

ENSG00000131097 ∙ NCBI:51751 ∙ ∙ HGNC:24318 ∙ Uniprot:Q9P298 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HIGD1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIGD1B 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in HIGD1B

This is a list of pathogenic ClinVar variants found in the HIGD1B region.

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

Position	Type	Phenotype	Significance	ClinVar
17-44849269-T-G		not specified	Uncertain significance (Feb 12, 2024)
17-44849307-C-T		not specified	Uncertain significance (Apr 07, 2023)
17-44849308-G-A		not specified	Uncertain significance (Feb 03, 2025)
17-44849314-C-T		not specified	Uncertain significance (May 04, 2022)
17-44849328-A-G		not specified	Uncertain significance (Dec 09, 2024)
17-44849383-T-A		not specified	Uncertain significance (Jan 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIGD1B	protein_coding	protein_coding	ENST00000253410	3	4128

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000391	0.229	125691	0	54	125745	0.000215

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.219	68	63.1	1.08	0.00000373	625
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000568	0.000568
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.000185	0.000185
European (Non-Finnish)	0.0000882	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000784	0.000784
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0751

Intolerance Scores

• loftool: 0.688
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.170
• ghis: 0.482

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Higd1b

Gene ontology

• Cellular component: integral component of membrane