ERMARD

ER membrane associated RNA degradation

Basic information

Region (hg38): 6:169751621-169781600

Previous symbols: [ "C6orf70" ]

Links

ENSG00000130023 ∙ NCBI:55780 ∙ OMIM:615532 ∙ HGNC:21056 ∙ Uniprot:Q5T6L9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• periventricular nodular heterotopia 6 (Limited), mode of inheritance: AD
• periventricular nodular heterotopia (Supportive), mode of inheritance: AD
• periventricular nodular heterotopia 6 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Periventricular nodular heterotopia 6	AD	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	Neurologic	24056535

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ERMARD 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			1	41	3	45
missense			92	12	9	113
nonsense		1	1			2
start loss						0
frameshift		1	7			8
inframe indel			1			1
splice donor/acceptor (+/-2bp)		2	4			6
splice region			1	5	3	9
non coding			4	34	36	74
Total	0	4	110	87	48

Variants in ERMARD

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

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

Position	Type	Phenotype	Significance	ClinVar
6-169751629-A-T			Likely benign (May 21, 2018)
6-169751645-G-C		not specified	Likely benign (Nov 14, 2017)
6-169751662-A-T		not specified	Benign (Oct 19, 2023)
6-169751670-C-T		not specified	Benign (Feb 01, 2024)
6-169751673-G-T			Likely benign (Jul 01, 2022)
6-169751675-G-A			Benign (Oct 31, 2022)
6-169751678-G-C			Likely benign (Oct 11, 2023)
6-169751681-C-T			Likely benign (Oct 03, 2023)
6-169751682-C-T		not specified	Likely benign (Apr 24, 2017)
6-169751683-C-T			Likely benign (Dec 02, 2021)
6-169753606-A-C			Benign (Jun 26, 2018)
6-169753840-CTTTTA-C		ERMARD-related disorder	Likely benign (Jan 10, 2024)
6-169753842-TTTA-T			Likely benign (Nov 28, 2023)
6-169753866-A-C		not specified	Benign (Jan 25, 2024)
6-169753889-CAT-C			Conflicting classifications of pathogenicity (Sep 01, 2022)
6-169753925-A-G			Uncertain significance (Mar 20, 2023)
6-169753946-A-G		not specified	Uncertain significance (Jun 08, 2022)
6-169753948-A-G		not specified	Uncertain significance (Sep 20, 2023)
6-169753957-A-G			Uncertain significance (Sep 01, 2022)
6-169753960-A-C			Uncertain significance (Oct 17, 2022)
6-169753973-C-G		not specified	Uncertain significance (Nov 02, 2023)
6-169753995-G-C			Uncertain significance (Apr 17, 2021)
6-169754000-C-T		not specified	Uncertain significance (Dec 17, 2023)
6-169754027-A-G		not specified	Uncertain significance (Mar 29, 2023)
6-169754028-G-C		not specified	Likely benign (Nov 29, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ERMARD	protein_coding	protein_coding	ENST00000366773	18	29963

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.78e-16	0.320	125370	1	377	125748	0.00150

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.320	384	367	1.05	0.0000203	4410
Missense in Polyphen		96	101.71	0.9439		1268
Synonymous	-0.398	145	139	1.04	0.00000800	1298
Loss of Function	1.44	29	38.6	0.750	0.00000199	464

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00396	0.00396
Ashkenazi Jewish	0.00	0.00
East Asian	0.00119	0.00114
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00167	0.00165
Middle Eastern	0.00119	0.00114
South Asian	0.00122	0.00118
Other	0.00164	0.00163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in neuronal migration during embryonic development. {ECO:0000269|PubMed:24056535}.
• Disease: DISEASE: Periventricular nodular heterotopia 6 (PVNH6) [MIM:615544]: A form of periventricular nodular heterotopia, a disorder resulting from a defect in the pattern of neuronal migration in which ectopic collections of neurons lie along the lateral ventricles of the brain or just beneath, contiguously or in isolated patches. PVNH6 results in delayed psychomotor development, delayed speech, strabismus, and onset of seizures with hypsarrhythmia in early infancy. {ECO:0000269|PubMed:24056535}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.0933

Intolerance Scores

• rvis_EVS: 1.43
• rvis_percentile_EVS: 94.99

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.180
• ghis: 0.441

Essentials

• essential_gene_CRISPR: 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: Ermard

Gene ontology

• Biological process: multicellular organism development;biological_process
• Cellular component: endoplasmic reticulum membrane;integral component of membrane
• Molecular function: molecular_function