FSIP2

fibrous sheath interacting protein 2

Basic information

Region (hg38): 2:185738804-185833290

Links

ENSG00000188738 ∙ NCBI:401024 ∙ OMIM:615796 ∙ HGNC:21675 ∙ Uniprot:Q5CZC0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• non-syndromic male infertility due to sperm motility disorder (Supportive), mode of inheritance: AR
• spermatogenic failure 34 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 34	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Genitourinary	30137358

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FSIP2 gene.

• Abnormal sperm morphology;Reduced sperm motility;Oligospermia (1 variants)
• Spermatogenic failure 34 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FSIP2 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				23	1	24
missense			534	49		583
nonsense						0
start loss						0
frameshift	2	3	1			6
inframe indel				1		1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			6			6
Total	2	3	541	73	1

Variants in FSIP2

This is a list of pathogenic ClinVar variants found in the FSIP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-185738832-A-C		not specified	Uncertain significance (Mar 01, 2023)
2-185738835-G-A		not specified	Uncertain significance (Jun 28, 2022)
2-185738851-A-G		not specified	Uncertain significance (Feb 27, 2023)
2-185738857-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-185738863-G-T		not specified	Uncertain significance (Mar 02, 2023)
2-185738884-C-T		not specified	Uncertain significance (Oct 24, 2023)
2-185738891-G-A		FSIP2-related disorder	Likely benign (Apr 11, 2019)
2-185738911-G-A		not specified	Uncertain significance (May 18, 2023)
2-185738980-A-G		not specified	Uncertain significance (Oct 30, 2023)
2-185738985-T-C		not specified	Uncertain significance (Feb 14, 2023)
2-185738993-C-T		FSIP2-related disorder	Likely benign (Apr 26, 2019)
2-185739377-G-A		not specified	Uncertain significance (Nov 07, 2022)
2-185739417-G-T			Likely benign (Dec 01, 2022)
2-185739439-G-A		not specified	Likely benign (Jun 10, 2024)
2-185743179-G-A			Uncertain significance (Mar 01, 2021)
2-185743184-T-C		FSIP2-related disorder	Likely benign (Apr 11, 2019)
2-185743216-A-T			Likely benign (Nov 01, 2024)
2-185744351-G-A		FSIP2-related disorder	Likely benign (Jan 02, 2020)
2-185745523-A-T		not specified	Uncertain significance (Jul 05, 2024)
2-185745528-A-C		not specified	Uncertain significance (Jul 27, 2022)
2-185745537-A-G		not specified	Uncertain significance (Feb 27, 2024)
2-185745553-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-185746709-C-T		not specified	Uncertain significance (May 14, 2024)
2-185746758-G-A			Uncertain significance (-)
2-185746761-A-G		not specified	Uncertain significance (Feb 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FSIP2	protein_coding	protein_coding	ENST00000343098	23	94663

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.63e-28	1.00	123370	0	10	123380	0.0000405

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.31	2489	3.00e+3	0.830	0.000142	46142
Missense in Polyphen		574	746.05	0.76939		12660
Synonymous	3.77	930	1.09e+3	0.854	0.0000533	12966
Loss of Function	7.35	81	190	0.425	0.00000924	3457

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000974	0.0000970
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000608	0.0000557
Finnish	0.0000472	0.0000464
European (Non-Finnish)	0.0000472	0.0000452
Middle Eastern	0.0000608	0.0000557
South Asian	0.0000340	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0762

Haploinsufficiency Scores

• pHI: 0.0521
• hipred: N
• hipred_score: 0.406

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.501

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fsip2