SPATA31F1

SPATA31 subfamily F member 1

Basic information

Region (hg38): 9:34723052-34729488

Previous symbols: [ "FAM205A" ]

Links

ENSG00000205108 ∙ NCBI:259308 ∙ ∙ HGNC:41911 ∙ Uniprot:Q6ZU69 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SPATA31F1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SPATA31F1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			82	10	3	95
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	82	13	3

Variants in SPATA31F1

This is a list of pathogenic ClinVar variants found in the SPATA31F1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-34723254-T-G		Abnormality of neuronal migration	Benign (Oct 31, 2014)
9-34723261-A-C		not specified	Uncertain significance (Feb 27, 2023)
9-34723282-G-A		not specified	Uncertain significance (Feb 21, 2024)
9-34723294-G-C		not specified	Uncertain significance (Mar 24, 2023)
9-34723296-G-T		not specified	Uncertain significance (Dec 03, 2021)
9-34723300-A-G		not specified	Likely benign (Apr 07, 2022)
9-34723305-A-G		not specified	Likely benign (Oct 10, 2023)
9-34723309-C-G		not specified	Uncertain significance (Dec 16, 2022)
9-34723342-G-C		not specified	Uncertain significance (Jan 02, 2024)
9-34723359-G-T		not specified	Uncertain significance (Oct 06, 2022)
9-34723372-C-G		not specified	Uncertain significance (Dec 21, 2022)
9-34723401-G-T		not specified	Uncertain significance (Dec 22, 2023)
9-34723482-C-G		not specified	Uncertain significance (Jun 30, 2022)
9-34723548-T-C		not specified	Uncertain significance (Aug 08, 2023)
9-34723621-T-G		Abnormality of neuronal migration	Benign (Oct 31, 2014)
9-34723629-G-T		not specified	Uncertain significance (Sep 26, 2023)
9-34723642-C-T		not specified	Likely benign (Oct 13, 2023)
9-34723644-T-G		not specified	Uncertain significance (Jun 30, 2023)
9-34723677-C-T		not specified	Uncertain significance (Jun 16, 2024)
9-34723678-C-A		not specified	Uncertain significance (May 01, 2024)
9-34723708-C-T		not specified	Uncertain significance (Mar 16, 2022)
9-34723758-A-G		not specified	Uncertain significance (Dec 11, 2023)
9-34723767-G-A		not specified	Uncertain significance (Aug 16, 2021)
9-34723860-C-T		not specified	Uncertain significance (Aug 15, 2023)
9-34723885-G-A		not specified	Uncertain significance (Oct 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SPATA31F1	protein_coding	protein_coding	ENST00000378788	4	6413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.321	0.679	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.67	530	650	0.816	0.0000322	8582
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 2.68
• rvis_percentile_EVS: 98.87

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam205a4

Gene ontology

• Cellular component: nucleus;integral component of membrane