BAIAP2L1

protein-coding

BAR/IMD domain containing adaptor protein 2 like 1, the group of I-BAR domain containing

Gene summary

This gene encodes a member of the IMD (IRSp53/MIM homology domain) family. Members of this family can be subdivided in two groups, the IRSp53-like and MIM-like, based on the presence or absence of the SH3 (Src homology 3) domain. The protein encoded by this gene contains a conserved IMD, also known as F-actin bundling domain, at the N-terminus, and a canonical SH3 domain near the C-terminus, so it belongs to the IRSp53-like group. This protein is the substrate for insulin receptor tyrosine kinase and binds to the small GTPase Rac. It is involved in signal transduction pathways that link deformation of the plasma membrane and remodeling of the actin cytoskeleton. It also promotes actin assembly and membrane protrusions when overexpressed in mammalian cells, and is essential to the formation of a potent actin assembly complex during EHEC (Enterohemorrhagic Escherichia coli) pedestal formation. [provided by RefSeq, Oct 2009]

MANE transcript

NM_018842.5

Inheritance

—

ClinVar variants

U:89B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.4

Max pathogenic AF

—

Genomic locus

chr7:98,291,650-98,401,090

External References & Databases

Ensembl (ENSG00000006453)

Transcript & Mutation Effects

hg38 • Region Span ~109.4 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 BAIAP2L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 88

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018842.5. 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	2 clinvar		3
missense			87 clinvar	2 clinvar		89
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	89	4	0	93

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018842.5	RefSeq	NP_061330.2	14	MANE Select
ENST00000005260.9	Ensembl	ENSP00000005260.8	14	MANE Select
ENST00000869912.1	Ensembl	ENSP00000539971.1	14	Standard
ENST00000869912.2	Ensembl	ENSP00000539971.1	14	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

EGFR1

Biological Process

plasma membrane organization
response to bacterium
positive regulation of actin filament polymerization
regulation of insulin receptor signaling pathway
actin filament bundle assembly

Molecular Function

actin binding
protein binding
proline-rich region binding
cadherin binding involved in cell-cell adhesion

Cellular Component

nucleoplasm
cytosol
plasma membrane
cell-cell adherens junction
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000005260
Coding exons: 14
Length: 109418
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125747
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.647	270	302	0.895	0.0000178	3331
Missense (PolyPhen)		98	127.2	0.77044		1435
Synonymous	-0.849	137	125	1.10	0.00000889	966
Loss of Function	3.04	12	29.9	0.401	0.00000172	351

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00050	0.00049	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00014	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May function as adapter protein. Involved in the formation of clusters of actin bundles. Plays a role in the reorganization of the actin cytoskeleton in response to bacterial infection. {ECO:0000269|PubMed:17430976, ECO:0000269|PubMed:19366662, ECO:0000269|PubMed:22921828}.;

Recessive Scores

pRec: 0.120

Intolerance Scores

LoFtool: 0.650
RVIS EVS: -0.55
RVIS percentile EVS: 19.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.815

Gene Damage Prediction

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