HIGD2A

HIG1 hypoxia inducible domain family member 2A, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 5:176388750-176389761

Links

ENSG00000146066 ∙ NCBI:192286 ∙ ∙ HGNC:28311 ∙ Uniprot:Q9BW72 ∙ 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 HIGD2A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HIGD2A 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			6	1		7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in HIGD2A

This is a list of pathogenic ClinVar variants found in the HIGD2A region.

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

Position	Type	Phenotype	Significance	ClinVar
5-176388844-C-A		not specified	Uncertain significance (Apr 22, 2022)
5-176388893-G-A		not specified	Uncertain significance (Oct 04, 2022)
5-176388909-G-C		not specified	Likely benign (Feb 27, 2023)
5-176388917-A-C		not specified	Uncertain significance (Oct 02, 2023)
5-176388950-G-A		not specified	Uncertain significance (Jul 30, 2023)
5-176388952-G-C		not specified	Uncertain significance (Oct 13, 2023)
5-176388959-C-T		not specified	Uncertain significance (Sep 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HIGD2A	protein_coding	protein_coding	ENST00000274787	2	1025

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.191	0.659	125722	0	12	125734	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.398	57	66.1	0.862	0.00000291	672
Missense in Polyphen		17	18.966	0.89632		211
Synonymous	-0.306	30	27.9	1.07	0.00000126	239
Loss of Function	0.939	1	2.65	0.378	1.12e-7	32

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000352	0.000351
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed subunit of cytochrome c oxidase (COX, complex IV), which is the terminal component of the mitochondrial respiratory chain that catalyzes the reduction of oxygen to water. May be involved in cytochrome c oxidase activity. May play a role in the assembly of respiratory supercomplexes. {ECO:0000269|PubMed:22342701}.

Recessive Scores

• pRec: 0.0768

Intolerance Scores

• loftool: 0.407
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.63

Haploinsufficiency Scores

• pHI: 0.0379
• hipred: N
• hipred_score: 0.187
• ghis: 0.526

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.723

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Higd2a

Gene ontology

• Biological process: negative regulation of apoptotic process;oxidation-reduction process
• Cellular component: mitochondrial inner membrane;integral component of membrane;respirasome