MFAP3L

protein-coding

microfibril associated protein 3 like, the group of I-set domain containing

Gene summary

Located in several cellular components, including cell junction; nucleoplasm; and plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_021647.8

Inheritance

—

ClinVar variants

U:47B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr4:169,986,597-170,033,031

External References & Databases

Ensembl (ENSG00000198948)

Transcript & Mutation Effects

hg38 • Region Span ~46.4 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 MFAP3L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 50

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_021647.8. 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			1
missense			46 clinvar	4 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	4	0	51

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_021647.8	RefSeq	NP_067679.6	2	MANE Select
ENST00000361618.4	Ensembl	ENSP00000354583.3	2	MANE Select
NM_001009554.4	RefSeq	NP_001009554.1	1	Standard
NM_001301647.2	RefSeq	NP_001288576.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding

Cellular Component

nucleus
cytoplasm
plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361618
Coding exons: 2
Length: 46435
Individuals with no LoFs: 125726
Homozygous LoFs: 0
Heterozygous LoFs: 7
Defined: 125733
p: 0.0000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.42	181	243	0.744	0.0000145	2685
Missense (PolyPhen)		51	100.99	0.50498		1048
Synonymous	-0.563	115	108	1.07	0.00000769	832
Loss of Function	2.84	1	11.3	0.0885	6.35e-7	137

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May participate in the nuclear signaling of EGFR and MAPK1/ERK2. May a have a role in metastasis. {ECO:0000269|PubMed:24735981}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.0592
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: 0.140

Gene Damage Prediction

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