SCNM1

sodium channel modifier 1

Basic information

Region (hg38): 1:151156664-151170296

Links

ENSG00000163156 ∙ NCBI:79005 ∙ OMIM:608095 ∙ HGNC:23136 ∙ Uniprot:Q9BWG6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• orofaciodigital syndrome 19 (Limited), mode of inheritance: AR
• orofaciodigital syndrome 19 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Orofaciodigital syndrome XIX	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	Craniofacial; Dental; Musculoskeletal; Neurologic	36084634

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCNM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCNM1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in SCNM1

This is a list of pathogenic ClinVar variants found in the SCNM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-151158717-A-C		not specified	Uncertain significance (Oct 16, 2024)
1-151158739-G-C		not specified	Uncertain significance (Aug 12, 2021)
1-151158762-C-T		not specified	Uncertain significance (Dec 09, 2023)
1-151158768-G-A			Benign (Jan 02, 2019)
1-151158850-C-A		not specified	Uncertain significance (Dec 13, 2021)
1-151158862-G-C		not specified	Uncertain significance (Jun 18, 2021)
1-151158869-C-T		not specified	Uncertain significance (Jun 03, 2022)
1-151158870-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-151158923-A-G		not specified	Uncertain significance (Oct 01, 2024)
1-151158969-G-A		not specified	Uncertain significance (Oct 25, 2024)
1-151159031-G-A		not specified	Uncertain significance (Jun 18, 2021)
1-151159060-C-G			Benign (Dec 31, 2019)
1-151159067-C-T		not specified	Uncertain significance (Dec 07, 2024)
1-151159105-G-A			Benign (Jul 04, 2018)
1-151159128-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-151159133-G-A		not specified	Uncertain significance (Feb 01, 2023)
1-151159177-T-A		not specified	Uncertain significance (Dec 11, 2023)
1-151159223-A-G		not specified	Uncertain significance (May 06, 2024)
1-151160913-C-T		not specified	Uncertain significance (May 01, 2024)
1-151160928-C-T		not specified	Uncertain significance (Apr 11, 2023)
1-151160937-C-T		not specified	Uncertain significance (Aug 07, 2024)
1-151160976-A-G		not specified	Uncertain significance (Aug 05, 2024)
1-151161872-C-G		not specified	Uncertain significance (Jan 26, 2022)
1-151161928-G-A		not specified	Uncertain significance (Jun 07, 2024)
1-151161944-T-A		not specified	Uncertain significance (Jun 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCNM1	protein_coding	protein_coding	ENST00000368905	7	13634

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000292	0.783	125703	0	44	125747	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.135	124	128	0.966	0.00000674	1474
Missense in Polyphen		61	62.036	0.9833		677
Synonymous	0.117	46	47.0	0.978	0.00000239	458
Loss of Function	1.28	11	16.6	0.661	0.00000120	156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000761	0.000760
Ashkenazi Jewish	0.000894	0.000893
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.0000796	0.0000791
Middle Eastern	0.000326	0.000326
South Asian	0.000134	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in RNA splicing, possibly contributing to the recognition of non-consensus donor sites. {ECO:0000250}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.496
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.18

Haploinsufficiency Scores

• pHI: 0.111
• hipred: N
• hipred_score: 0.212
• ghis: 0.521

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.907

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scnm1
• Phenotype: normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; muscle phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: alternative mRNA splicing, via spliceosome;RNA splicing
• Cellular component: nucleus;nuclear speck
• Molecular function: protein binding;enzyme binding;metal ion binding