BPIFA3

protein-coding

BPI fold containing family A member 3, the group of BPI fold containing

Gene summary

Predicted to enable lipid binding activity. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C20orf71

MANE transcript

NM_178466.5

Inheritance

—

ClinVar variants

U:36B:10

Top phenotype

BPIFA3-related disorder

gnomAD constraint

pLI —, LoF o/e 1.22

Max pathogenic AF

—

Genomic locus

chr20:33,217,310-33,227,806

External References & Databases

Ensembl (ENSG00000131059)

Transcript & Mutation Effects

hg38 • Region Span ~10.5 kb

Loading mutation effect viewer...

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 BPIFA3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 41

BPIFA3-related disorderTotal: 4

PreeclampsiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178466.5. 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						0
missense			35 clinvar	7 clinvar	1 clinvar	43
nonsense					2 clinvar	2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	36	7	3	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178466.5	RefSeq	NP_848561.2	7	MANE Select
ENST00000375454.8	Ensembl	ENSP00000364603.3	7	MANE Select
NM_001042439.2	RefSeq	NP_001035904.1	6	Standard
ENST00000375452.3	Ensembl	ENSP00000364601.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

lipid binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375454
Coding exons: 7
Length: 10449
Individuals with no LoFs: 125302
Homozygous LoFs: 5
Heterozygous LoFs: 435
Defined: 125742
p: 0.00175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.455	157	142	1.11	0.00000707	1689
Missense (PolyPhen)		40	37.479	1.0673		539
Synonymous	-0.521	60	55.1	1.09	0.00000306	470
Loss of Function	-0.748	17	14.0	1.22	7.81e-7	140

Population LoF Frequency

Population	CAF	p-value	Status
African	0.034	0.020	notable
Latino/Admixed American	0.0023	0.0013	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00056	0.00046	rare
South Asian	0.00046	0.00033	rare
Other	0.00082	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 1
RVIS percentile EVS: 90.62

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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