RMDN3

protein-coding

regulator of microtubule dynamics 3

Gene summary

Enables microtubule binding activity. Involved in intracellular calcium ion homeostasis. Located in several cellular components, including intercellular bridge; mitochondrial outer membrane; and spindle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM82C
FAM82A2

MANE transcript

NM_018145.3

Inheritance

—

ClinVar variants

U:71B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.43

Max pathogenic AF

—

Genomic locus

chr15:40,735,884-40,755,851

External References & Databases

Ensembl (ENSG00000137824)

Transcript & Mutation Effects

hg38 • Region Span ~20.0 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 RMDN3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 61

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018145.3. 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			3 clinvar			3
missense			66 clinvar	1 clinvar		67
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	71	1	0	72

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 54 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018145.3	RefSeq	NP_060615.1	12	MANE Select
ENST00000338376.8	Ensembl	ENSP00000342493.3	12	MANE Select
NM_001304802.2	RefSeq	NP_001291731.1	12	Standard
NM_001323894.2	RefSeq	NP_001310823.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cellular calcium ion homeostasis
apoptotic process
cell differentiation

Molecular Function

protein binding

Cellular Component

spindle pole
nucleus
mitochondrion
mitochondrial outer membrane
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000260385
Coding exons: 12
Length: 19968
Individuals with no LoFs: 125690
Homozygous LoFs: 0
Heterozygous LoFs: 58
Defined: 125748
p: 0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.388	254	272	0.934	0.0000153	3015
Missense (PolyPhen)		86	83.397	1.0312		925
Synonymous	0.411	103	108	0.950	0.00000577	955
Loss of Function	2.81	12	28.1	0.427	0.00000153	302

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.00069	0.00060	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00030	0.00029	rare
Other	0.00034	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in cellular calcium homeostasis regulation. May participate in differentiation and apoptosis of keratinocytes. Overexpression induces apoptosis. {ECO:0000269|PubMed:16820967, ECO:0000269|PubMed:22131369}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

RVIS EVS: -0.43
RVIS percentile EVS: 25.37

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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