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…

Primary Disease Associations & Inheritance

Orofaciodigital syndrome XIXMIM #620107

Clinical highlights

Gene–disease validity

Not independently assessedOMIM lists Orofaciodigital syndrome XIX; no ClinGen or GenCC tier

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.09

LOEUF

—

Mechanism

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

Background carrier burden — how many people carry a rare variant somewhere in SCNM1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 210

285 rare PASS variants

Rare truncating (LoF)

1 in 1,300

59 rare PASS variants

Rare synonymous (reference)

1 in 440

106 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for SCNM1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 190	1 in 1,900
South Asian	~43k	1 in 170	1 in 860
Remaining (unassigned)	~30k	1 in 230	1 in 630
European (Finnish)	~27k	1 in 570	none seen
Admixed American	~22k	1 in 290	1 in 1,400
African / African American	~21k	1 in 230	1 in 720
East Asian	~20k	1 in 280	1 in 920
Ashkenazi Jewish	~13k	1 in 620	1 in 540
Middle Eastern	~2,884	1 in 580	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 7 of 7 coding exons well covered in gnomAD exomes. Genomes: 6 of 7 (exon 7 below).? see exons ↓