RMDN3

regulator of microtubule dynamics 3

Basic information

Region (hg38): 15:40735883-40755851

Previous symbols: [ "FAM82C", "FAM82A2" ]

Links

ENSG00000137824 ∙ NCBI:55177 ∙ OMIM:611873 ∙ HGNC:25550 ∙ Uniprot:Q96TC7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RMDN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RMDN3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in RMDN3

This is a list of pathogenic ClinVar variants found in the RMDN3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-40737134-A-C		not specified	Uncertain significance (Jan 08, 2024)
15-40737159-T-G		not specified	Uncertain significance (Mar 17, 2023)
15-40737704-T-C		not specified	Uncertain significance (Mar 22, 2023)
15-40738000-T-G		not specified	Uncertain significance (Oct 12, 2021)
15-40738539-T-C		not specified	Likely benign (Apr 12, 2022)
15-40740184-T-G		not specified	Uncertain significance (Mar 29, 2022)
15-40744078-C-G		not specified	Uncertain significance (Mar 01, 2024)
15-40744122-G-A		not specified	Uncertain significance (Apr 25, 2022)
15-40744139-C-T		not specified	Uncertain significance (May 13, 2024)
15-40744140-G-A		not specified	Uncertain significance (May 03, 2023)
15-40744148-T-C		not specified	Uncertain significance (Nov 09, 2022)
15-40745020-C-G		not specified	Uncertain significance (Dec 16, 2023)
15-40745032-C-T		not specified	Uncertain significance (Jun 09, 2022)
15-40745045-C-G		not specified	Uncertain significance (May 09, 2023)
15-40745207-T-C		not specified	Uncertain significance (May 23, 2024)
15-40751454-T-G		not specified	Uncertain significance (Jun 16, 2024)
15-40751459-C-T		not specified	Uncertain significance (Aug 30, 2021)
15-40751471-G-A		not specified	Uncertain significance (Nov 17, 2022)
15-40751472-T-C		not specified	Uncertain significance (Nov 14, 2023)
15-40751522-G-A		not specified	Uncertain significance (Jun 06, 2022)
15-40752052-C-T		not specified	Uncertain significance (Nov 07, 2022)
15-40752111-T-A		not specified	Uncertain significance (Jan 03, 2022)
15-40752115-C-T		not specified	Uncertain significance (Jan 03, 2022)
15-40754729-C-A		not specified	Uncertain significance (Jan 26, 2023)
15-40754749-G-A		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RMDN3	protein_coding	protein_coding	ENST00000260385	12	19968

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000517	0.999	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.388	254	272	0.934	0.0000153	3015
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000608	0.000604
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000693	0.000601
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.0000544	0.0000544
South Asian	0.000296	0.000294
Other	0.000337	0.000326

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.170
• hipred: Y
• hipred_score: 0.655
• ghis: 0.576

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rmdn3
• Phenotype: normal phenotype

Gene ontology

• Biological process: cellular calcium ion homeostasis;apoptotic process;cell differentiation
• Cellular component: spindle pole;nucleus;mitochondrion;mitochondrial outer membrane;microtubule;integral component of membrane
• Molecular function: protein binding