ROGDI

rogdi atypical leucine zipper

Basic information

Region (hg38): 16:4796968-4802880

Links

ENSG00000067836 ∙ NCBI:79641 ∙ OMIM:614574 ∙ HGNC:29478 ∙ Uniprot:Q9GZN7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amelocerebrohypohidrotic syndrome (Definitive), mode of inheritance: AR
• amelocerebrohypohidrotic syndrome (Strong), mode of inheritance: AR
• amelocerebrohypohidrotic syndrome (Supportive), mode of inheritance: AR
• amelocerebrohypohidrotic syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Kohlschutter-Tonz syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Dental; Neurologic	4372200; 16411202; 22482807; 22424600

ClinVar

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

• Amelocerebrohypohidrotic syndrome (24 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ROGDI 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			2	108	4	114
missense			199	3	1	203
nonsense	13		1			14
start loss	1		2			3
frameshift	8	1	1			10
inframe indel			3			3
splice donor/acceptor (+/-2bp)	2	9				11
splice region		1	20	33	2	56
non coding		1	12	95	15	123
Total	24	11	220	206	20

Highest pathogenic variant AF is 0.0000329

Variants in ROGDI

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

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

Position	Type	Phenotype	Significance	ClinVar
16-4797006-C-T		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 13, 2018)
16-4797009-G-C		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 12, 2018)
16-4797080-C-T		Amelocerebrohypohidrotic syndrome	Likely benign (Apr 27, 2017)
16-4797105-C-A		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 12, 2018)
16-4797113-C-A		Amelocerebrohypohidrotic syndrome	Likely benign (Jan 12, 2018)
16-4797162-C-T		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 13, 2018)
16-4797168-G-A		Amelocerebrohypohidrotic syndrome	Benign (Apr 27, 2017)
16-4797190-A-G		Amelocerebrohypohidrotic syndrome	Benign (Jan 13, 2018)
16-4797214-C-T		Amelocerebrohypohidrotic syndrome	Uncertain significance (Mar 23, 2018)
16-4797252-C-T		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 12, 2018)
16-4797316-C-T		Amelocerebrohypohidrotic syndrome	Benign (May 14, 2021)
16-4797344-G-A			Benign (Feb 01, 2023)
16-4797348-G-A		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 13, 2018)
16-4797406-G-C		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 12, 2018)
16-4797416-G-C		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 13, 2018)
16-4797436-G-A		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jan 22, 2018)
16-4797465-A-G		Amelocerebrohypohidrotic syndrome • Inborn genetic diseases	Uncertain significance (Sep 07, 2022)
16-4797466-G-C		Amelocerebrohypohidrotic syndrome	Likely benign (Mar 25, 2021)
16-4797468-G-C		Amelocerebrohypohidrotic syndrome	Uncertain significance (Aug 18, 2021)
16-4797472-G-A		Amelocerebrohypohidrotic syndrome	Likely benign (Jan 11, 2022)
16-4797473-T-C		Amelocerebrohypohidrotic syndrome	Uncertain significance (Oct 14, 2022)
16-4797480-A-G		Amelocerebrohypohidrotic syndrome	Uncertain significance (May 27, 2022)
16-4797485-C-A		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jun 29, 2022)
16-4797486-T-C		Amelocerebrohypohidrotic syndrome	Uncertain significance (Jun 08, 2022)
16-4797487-G-T		Amelocerebrohypohidrotic syndrome	Likely benign (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ROGDI	protein_coding	protein_coding	ENST00000322048	11	5983

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.55e-9	0.154	125709	0	29	125738	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.32	212	164	1.29	0.0000102	1821
Missense in Polyphen		75	59.677	1.2568		664
Synonymous	-4.35	117	70.5	1.66	0.00000466	551
Loss of Function	0.325	14	15.4	0.911	6.57e-7	184

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000151
Ashkenazi Jewish	0.000299	0.000298
East Asian	0.000109	0.000109
Finnish	0.0000967	0.0000924
European (Non-Finnish)	0.0000898	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.000198	0.000196
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.737
• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.77

Haploinsufficiency Scores

• pHI: 0.170
• hipred: N
• hipred_score: 0.466
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.841

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rogdi

Gene ontology

• Biological process: vacuolar acidification;brain development;positive regulation of cell population proliferation;neurogenesis;hemopoiesis;developmental process;odontogenesis of dentin-containing tooth
• Cellular component: nucleus;nuclear envelope;synaptic vesicle;cell junction;axon;dendrite;presynaptic membrane;perikaryon;RAVE complex