GNB1L

protein-coding

G protein subunit beta 1 like, the group of WD repeat domain containing

Gene summary

This gene encodes a G-protein beta-subunit-like polypeptide which is a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein contains 6 WD repeats and is highly expressed in the heart. The gene maps to the region on chromosome 22q11, which is deleted in DiGeorge syndrome, trisomic in derivative 22 syndrome and tetrasomic in cat-eye syndrome. Therefore, this gene may contribute to the etiology of those disorders. Transcripts from this gene share exons with some transcripts from the C22orf29 gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_053004.3

Inheritance

—

ClinVar variants

U:74B:21

Top phenotype

GNB1L-related disorder

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr22:19,783,223-19,854,939

External References & Databases

Ensembl (ENSG00000185838)

Transcript & Mutation Effects

hg38 • Region Span ~71.7 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 GNB1L variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 72

not providedTotal: 15

GNB1L-related disorderTotal: 11

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_053004.3. 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				8 clinvar	5 clinvar	13
missense			72 clinvar	5 clinvar	3 clinvar	80
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	74	13	8	95

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 31 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_053004.3	RefSeq	NP_443730.1	6	MANE Select
ENST00000329517.11	Ensembl	ENSP00000331313.6	6	MANE Select
ENST00000403325.5	Ensembl	ENSP00000385154.1	6	Standard
ENST00000403325.6	Ensembl	ENSP00000385154.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Beta-agonist/Beta-blocker Pathway, Pharmacodynamics

Biological Process

G protein-coupled receptor signaling pathway
social behavior
intracellular signal transduction

Molecular Function

molecular_function

Cellular Component

cytoplasm
cytoplasmic side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000329517
Coding exons: 6
Length: 71716
Individuals with no LoFs: 125619
Homozygous LoFs: 0
Heterozygous LoFs: 105
Defined: 125724
p: 0.000418

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.0200	235	236	0.996	0.0000172	2089
Missense (PolyPhen)		49	55.345	0.88535		562
Synonymous	-0.251	112	109	1.03	0.00000848	703
Loss of Function	1.43	9	15.0	0.601	7.30e-7	140

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00055	0.00055	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.0024	0.0024	notable
European (Non-Finnish)	0.00024	0.00024	rare
South Asian	0.000098	0.000098	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.704
RVIS EVS: 0.69
RVIS percentile EVS: 85.18

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.994

Gene Damage Prediction

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