SMTNL1

Chr 11

smoothelin like 1

Also known as: CHASM

NCBI Gene: 219537 ENSG00000214872 UniProt: A8MU46

The protein encoded by this gene is involved in the contraction of both striated and smooth muscle. During pregnancy, the encoded protein interacts with progesterone receptor to attenuate the expression of contractile and metabolic proteins. [provided by RefSeq, Jul 2016]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.33

LOEUF

—

Mechanism

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.33LOEUF

pLI 0.000

Z-score 0.41

OE 0.90 (0.63–1.33)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.43Z-score

OE missense 0.93 (0.84–1.03)

271 obs / 291.5 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.90 (0.63–1.33)

0≤0.351.4

Missense OE?0.93 (0.84–1.03)

0≤0.61.4

Synonymous OE?1.14

0≤1.21.6

LoF obs/exp: 19 / 21.0Missense obs/exp: 271 / 291.5Syn Z: -1.21

Background carrier burden — how many people carry a rare variant somewhere in SMTNL1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 89

638 rare PASS variants

Rare truncating (LoF)

1 in 430

114 rare PASS variants

Rare synonymous (reference)

1 in 200

250 rare PASS variants

Rare missense and truncating variants are carried at similar rates in SMTNL1; this gene does not show strong loss-of-function constraint by this measure. 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 120	1 in 700
South Asian	~43k	1 in 64	1 in 420
Remaining (unassigned)	~30k	1 in 84	1 in 230
European (Finnish)	~27k	1 in 560	1 in 1,900
Admixed American	~22k	1 in 79	1 in 510
African / African American	~21k	1 in 70	1 in 850
East Asian	~20k	1 in 86	1 in 680
Ashkenazi Jewish	~13k	1 in 290	≈ 1 in 4,300
Middle Eastern	~2,884	1 in 88	1 in 570

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): All 7 coding exons well covered in gnomAD exomes and genomes.? see exons ↓