SP5

Chr 2

Sp5 transcription factor

NCBI Gene: 389058 ENSG00000204335 UniProt: Q6BEB4 OMIM: 609391

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within bone morphogenesis and post-anal tail morphogenesis. Predicted to be located in chromatin. [provided by Alliance of Genome Resources, Jul 2025]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOFmechanismLOEUF 0.59

Clinical Summary— SP5

⚡

Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.52) — some intolerance to loss-of-function variants.

📋

ClinVar Variants

62 VUS of 63 total submissions

Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Moderate LoF intolerance

LoF Constraint?

0.59LOEUF

pLI 0.518

Z-score 2.45

OE 0.19 (0.08–0.59)

Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?

-0.02Z-score

OE missense 1.00 (0.90–1.12)

222 obs / 221.3 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.19 (0.08–0.59)

0≤0.351.4

Missense OE?1.00 (0.90–1.12)

0≤0.61.4

Synonymous OE?1.17

0≤1.21.6

LoF obs/exp: 2 / 10.6Missense obs/exp: 222 / 221.3Syn Z: -1.41

This gene — mechanism propensity

0.6065th %ile

GOF

0.3094th %ile

LOF

0.74top 10%

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

LOFprediction above median

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

63 submitted variants in ClinVar

ClinVar

Classification Summary

VUS62

VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	62	62
Likely Benign	0	0
Benign	0	0
Total	62	62

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

View in ClinVar →

19 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap SP5 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →