SPATA31F1

Chr 9

SPATA31 subfamily F member 1

Also known as: C9orf144B, FAM205A

NCBI Gene: 259308ENSG00000205108UniProt: Q6ZU69

SPATA31F1 encodes a nuclear protein whose specific function is not well characterized. The gene shows high constraint against loss-of-function variants (LOEUF 0.414), suggesting it is critical for normal cellular function, but no definitive disease associations have been established in humans. Clinical significance of variants in this gene remains unclear pending further research.

ResearchSummary from RefSeq
MultiplemechanismLOEUF 0.41
Clinical Summary— SPATA31F1
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.23) despite low pLI — interpret in context.
📋
ClinVar Variants
71 unique Pathogenic / Likely Pathogenic· 192 VUS of 295 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
0.41LOEUF
pLI 0.321
Z-score 4.21
OE 0.23 (0.13–0.41)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.67Z-score
OE missense 0.82 (0.76–0.88)
530 obs / 649.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.23 (0.13–0.41)
0≤0.351.4
Missense OE0.82 (0.76–0.88)
0≤0.61.4
Synonymous OE0.73
0≤1.21.6
LoF obs/exp: 8 / 34.8Missense obs/exp: 530 / 649.6Syn Z: 3.41
DN
0.76top 25%
GOF
0.84top 5%
LOF
0.2971th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

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

ClinVar Variant Classifications

295 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic63
Likely Pathogenic8
VUS192
Likely Benign23
Benign8
63
Pathogenic
8
Likely Pathogenic
192
VUS
23
Likely Benign
8
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
63
0
63
Likely Pathogenic
0
0
8
0
8
VUS
0
181
11
0
192
Likely Benign
0
20
0
3
23
Benign
0
8
0
0
8
Total0209823294

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

View in ClinVar →

Protein Context — Lollipop Plot

SPATA31F1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
Open Research Assistant →

No publications found for SPATA31F1

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients