GPHA2

glycoprotein hormone subunit alpha 2, the group of Glycoprotein hormone subunits

Basic information

Region (hg38): 11:64934471-64935893

Links

ENSG00000149735 ∙ NCBI:170589 ∙ OMIM:609651 ∙ HGNC:18054 ∙ Uniprot:Q96T91 ∙ 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 GPHA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPHA2 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			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in GPHA2

This is a list of pathogenic ClinVar variants found in the GPHA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-64934781-G-A		not specified	Uncertain significance (Nov 16, 2021)
11-64934789-C-A		not specified	Uncertain significance (Dec 20, 2023)
11-64934789-C-G		not specified	Uncertain significance (Aug 05, 2024)
11-64934790-G-A		not specified	Uncertain significance (Mar 01, 2023)
11-64934816-G-T		not specified	Uncertain significance (Sep 11, 2024)
11-64934832-G-A		not specified	Uncertain significance (Feb 21, 2025)
11-64934844-G-A		not specified	Uncertain significance (Oct 28, 2023)
11-64935149-G-A		not specified	Uncertain significance (Nov 29, 2023)
11-64935157-C-T		not specified	Uncertain significance (Oct 06, 2022)
11-64935405-G-T		not specified	Uncertain significance (Jan 16, 2024)
11-64935426-T-C		not specified	Likely benign (Sep 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPHA2	protein_coding	protein_coding	ENST00000279168	3	1418

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-8	0.0328	125592	1	155	125748	0.000620

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0897	75	77.2	0.971	0.00000491	821
Missense in Polyphen		38	33.643	1.1295		365
Synonymous	0.605	27	31.3	0.862	0.00000185	272
Loss of Function	-1.27	10	6.51	1.54	4.49e-7	56

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00111	0.00111
Ashkenazi Jewish	0.00	0.00
East Asian	0.000707	0.000707
Finnish	0.00296	0.00291
European (Non-Finnish)	0.000415	0.000413
Middle Eastern	0.000707	0.000707
South Asian	0.0000385	0.0000327
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functions as a heterodimeric glycoprotein hormone with GPHB5 able to bind and activate the thyroid-stimulating hormone receptor (TSHR), leading to increased cAMP production (PubMed:12045258). Plays a central role in controlling thyroid cell metabolism (PubMed:12045258). {ECO:0000269|PubMed:12045258}.
• Pathway: Signaling by GPCR;Signal Transduction;G alpha (s) signalling events;Hormone ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.648
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.276
• hipred: N
• hipred_score: 0.167
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpha2

Gene ontology

• Biological process: cell surface receptor signaling pathway;G protein-coupled receptor signaling pathway;adenylate cyclase-activating G protein-coupled receptor signaling pathway;regulation of signaling receptor activity
• Cellular component: extracellular region;extracellular space
• Molecular function: hormone activity;protein binding;thyrotropin-releasing hormone receptor binding;protein heterodimerization activity;hormone receptor binding