SCRT1

Chr 8

scratch family transcriptional repressor 1

Also known as: SCRT, ZNF898

NCBI Gene: 83482 ENSG00000261678 UniProt: Q9BWW7 OMIM: 605858

This gene encodes a C2H2-type zinc finger transcriptional repressor that binds to E-box motifs and modulates basic helix-loop-helix transcription factors critical for neuronal differentiation. Mutations cause neurodevelopmental disorder with or without anomalies of the brain, eye, or heart, which follows an autosomal dominant inheritance pattern. The gene shows tolerance to loss-of-function variants, suggesting the disorder may involve complex mutational mechanisms.

OMIM ResearchSummary from RefSeq, UniProt

This gene encodes a C2H2-type zinc finger transcriptional repressor that binds to E-box motifs. The encoded protein may promote neural differention and may be involved in cancers with neuroendocrine features. [provided by RefSeq, Jul 2013]

OMIM ResearchGenerating clinical summary…

LOEUF 0.88

Clinical Summary— SCRT1

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.28) despite low pLI — interpret in context.

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ClinVar Variants

38 VUS of 40 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?

0.88LOEUF

pLI 0.222

Z-score 1.78

OE 0.28 (0.11–0.88)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

2.43Z-score

OE missense 0.45 (0.37–0.55)

68 obs / 152.5 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?

LoF OE?0.28 (0.11–0.88)

0≤0.351.4

Missense OE?0.45 (0.37–0.55)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 2 / 7.1Missense obs/exp: 68 / 152.5Syn Z: 0.24

ClinVar Variant Classifications

40 submitted variants in ClinVar

ClinVar

Classification Summary

VUS38

Likely Benign1

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	38	0	38
Likely Benign	0	1	1
Benign	0	0	0
Total	38	1	39

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

View in ClinVar →

57 pathogenic / likely-pathogenic (of 72) ClinVar copy-number / structural variants overlap SCRT1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →