SPATA31F1

protein-coding

SPATA31 subfamily F member 1

Gene summary

Located in nucleus. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM205A

MANE transcript

NM_001141917.2

Inheritance

—

ClinVar variants

U:181B:29

Top phenotype

Abnormality of neuronal migration

gnomAD constraint

pLI —, LoF o/e 0.23

Max pathogenic AF

—

Genomic locus

chr9:34,723,053-34,729,488

External References & Databases

Ensembl (ENSG00000205108)

Transcript & Mutation Effects

hg38 • Region Span ~6.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SPATA31F1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 201

Abnormality of neuronal migrationTotal: 5

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001141917.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			181 clinvar	20 clinvar	6 clinvar	207
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	181	23	6	210

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001141917.2	RefSeq	NP_001135389.1	4	MANE Select
ENST00000378788.4	Ensembl	ENSP00000417711.1	4	MANE Select
ENST00001128267.1	Ensembl	ENSP00000798072.1	5	Standard
ENST00001128268.1	Ensembl	ENSP00000798073.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

nucleus
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378788
Coding exons: 4
Length: 6413
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.67	530	650	0.816	0.0000322	8582
Missense (PolyPhen)		153	190.92	0.8014		2827
Synonymous	3.41	193	263	0.733	0.0000135	2737
Loss of Function	4.21	8	34.8	0.230	0.00000175	407

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: 2.68
RVIS percentile EVS: 98.87

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High