SWT1

Chr 1

SWT1 RNA endoribonuclease homolog

Also known as: C1orf26, HsSwt1

NCBI Gene: 54823 ENSG00000116668 UniProt: Q5T5J6 OMIM: 619513

Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.27

Clinical Summary— SWT1

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.

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ClinVar Variants

96 VUS of 134 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?

0.27LOEUF

pLI 0.998

Z-score 5.32

OE 0.14 (0.07–0.27)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?

1.49Z-score

OE missense 0.80 (0.73–0.87)

344 obs / 430.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.14 (0.07–0.27)

0≤0.351.4

Missense OE?0.80 (0.73–0.87)

0≤0.61.4

Synonymous OE?0.95

0≤1.21.6

LoF obs/exp: 6 / 44.1Missense obs/exp: 344 / 430.9Syn Z: 0.50

This gene — mechanism propensity

0.3991th %ile

GOF

0.3094th %ile

LOF

0.68top 10%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.27

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

134 submitted variants in ClinVar

ClinVar

Classification Summary

VUS96

Likely Benign16

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0
Likely Pathogenic	0	0	0	0
VUS	95	1	0	96
Likely Benign	15	0	1	16
Benign	0	0	0	0
Total	110	1	1	112

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

View in ClinVar →

25 pathogenic / likely-pathogenic (of 28) ClinVar copy-number / structural variants overlap SWT1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →