BAIAP2L2

protein-coding

BAR/IMD domain containing adaptor protein 2 like 2, the group of I-BAR domain containing

Gene summary

The protein encoded by this gene binds phosphoinositides and promotes the formation of planar or curved membrane structures. The encoded protein is found in RAB13-positive vesicles and at intercellular contacts with the plasma membrane. [provided by RefSeq, Dec 2012]

MANE transcript

NM_025045.6

Inheritance

—

ClinVar variants

U:120B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr22:38,084,652-38,111,015

External References & Databases

Ensembl (ENSG00000128298)

Transcript & Mutation Effects

hg38 • Region Span ~26.4 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 BAIAP2L2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 117

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_025045.6. 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			1 clinvar	3 clinvar		4
missense			116 clinvar	3 clinvar		119
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	120	6	0	126

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_025045.6	RefSeq	NP_079321.3	14	MANE Select
ENST00000381669.8	Ensembl	ENSP00000371085.3	14	MANE Select
ENST00000332536.10	Ensembl	ENSP00000328876.7	9	Standard
ENST00000428572.1	Ensembl	ENSP00000410074.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

plasma membrane organization
positive regulation of actin filament polymerization
actin filament bundle assembly
actin crosslink formation
membrane organization

Molecular Function

phospholipid binding

Cellular Component

nucleoplasm
cytosol
plasma membrane
vesicle membrane
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381669
Coding exons: 14
Length: 25782
Individuals with no LoFs: 124650
Homozygous LoFs: 1
Heterozygous LoFs: 153
Defined: 124804
p: 0.000617

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.239	283	295	0.961	0.0000200	3371
Missense (PolyPhen)		93	102.85	0.90426		1048
Synonymous	-0.0778	114	113	1.01	0.00000746	1065
Loss of Function	1.20	17	23.2	0.732	0.00000113	296

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00035	0.00026	rare
Latino/Admixed American	0.00063	0.00043	rare
Ashkenazi Jewish	0.00032	0.00020	rare
East Asian	0.0010	0.0010	notable
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00077	0.00048	rare
South Asian	0.0035	0.0020	notable
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Phosphoinositides-binding protein that induces the formation of planar or gently curved membrane structures. Binds to phosphoinositides, including to phosphatidylinositol 4,5- bisphosphate (PtdIns(4,5)P2) headgroups. There seems to be no clear preference for a specific phosphoinositide (By similarity). {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.398
RVIS EVS: -0.45
RVIS percentile EVS: 24.19

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.245

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High