SCNM1

Chr 1AR

sodium channel modifier 1

Also known as: OFD19

NCBI Gene: 79005 ENSG00000163156 UniProt: Q9BWG6 OMIM: 608095

SCNM1 is a zinc finger protein and putative splicing factor. In mice, Scnm1 modifies phenotypic expression of Scn8a (MIM 600702) mutations (Buchner et al., 2003 [PubMed 12920299]).[supplied by OMIM, Oct 2009]

OMIM Research

OMIM ResearchGenerating clinical summary…

ARLOEUF 1.091 OMIM phenotype

Clinical Summary— SCNM1

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

3 unique Pathogenic / Likely Pathogenic· 34 VUS of 43 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.09LOEUF

pLI 0.000

Z-score 1.28

OE 0.66 (0.41–1.09)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.13Z-score

OE missense 0.97 (0.83–1.12)

124 obs / 128.3 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.66 (0.41–1.09)

0≤0.351.4

Missense OE?0.97 (0.83–1.12)

0≤0.61.4

Synonymous OE?0.98

0≤1.21.6

LoF obs/exp: 11 / 16.6Missense obs/exp: 124 / 128.3Syn Z: 0.12

ClinVar Variant Classifications

43 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic3

VUS34

Likely Benign4

Pathogenic

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	1	1	0	3
Likely Pathogenic	0	0	0	0	0
VUS	1	33	0	0	34
Likely Benign	0	2	1	1	4
Benign	0	0	0	0	0
Total	2	36	2	1	41

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

15 pathogenic / likely-pathogenic (of 18) ClinVar copy-number / structural variants overlap SCNM1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →