RFLNA

protein-coding

refilin A

Gene summary

Predicted to enable filamin binding activity. Predicted to be involved in several processes, including actin filament bundle organization; negative regulation of bone mineralization involved in bone maturation; and negative regulation of chondrocyte development. Predicted to be located in cytoskeleton. Predicted to be active in actin filament bundle. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM101A

MANE transcript

NM_001365156.1

Inheritance

—

ClinVar variants

U:1B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr12:123,973,241-124,316,024

External References & Databases

Ensembl (ENSG00000178882)

Transcript & Mutation Effects

hg38 • Region Span ~342.8 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 RFLNA variants in ClinVar

1 Conditions Cataloged

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001365156.1. 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						0
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	1	1	0	2

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001365156.1	RefSeq	NP_001352085.1	3	MANE Select
ENST00000546355.4	Ensembl	ENSP00000444080.2	3	MANE Select
NM_181709.5	RefSeq	NP_859060.3	2	Standard
ENST00000324038.6	Ensembl	ENSP00000315626.3	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

skeletal system morphogenesis
negative regulation of chondrocyte development
actin filament bundle organization
negative regulation of bone mineralization involved in bone maturation

Molecular Function

protein binding
filamin binding

Cellular Component

cytoplasm
actin filament bundle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000324038
Coding exons: 2
Length: 342783
Individuals with no LoFs: 125537
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125540
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.390	86	96.8	0.888	0.00000745	870
Missense (PolyPhen)		29	39.966	0.72562		380
Synonymous	-0.146	42	40.8	1.03	0.00000296	283
Loss of Function	1.14	1	3.19	0.313	1.36e-7	38

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000038	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the regulation of the perinuclear actin network and nuclear shape through interaction with filamins. Plays an essential role in actin cytoskeleton formation in developing cartilaginous cells. {ECO:0000250|UniProtKB:Q7TS73}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

RVIS EVS: 0.68
RVIS percentile EVS: 84.93

Essentials

Essential (gene trap): N