C14orf39

chromosome 14 open reading frame 39

Basic information

Region (hg38): 14:60396469-60515543

Links

ENSG00000179008 ∙ NCBI:317761 ∙ OMIM:617307 ∙ HGNC:19849 ∙ Uniprot:Q8N1H7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 52 (Limited), mode of inheritance: Unknown
• premature ovarian failure 18 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 52; Premature ovarian failure 18	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; Obstetric	33508233

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C14orf39 gene.

• not_provided (7 variants)
• Spermatogenic_failure_52 (5 variants)
• not_specified (4 variants)
• Non-obstructive_azoospermia (3 variants)
• Premature_ovarian_failure_18 (2 variants)
• C14orf39-related_disorder (1 variants)
• Inherited_primary_ovarian_failure (1 variants)
• Azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C14orf39 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000174978.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3		3
missense			4	3	1	8
nonsense	1					1
start loss						0
frameshift	2	1				3
splice donor/acceptor (+/-2bp)						0
Total	3	1	4	6	1

Highest pathogenic variant AF is 0.0000180019

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C14orf39	protein_coding	protein_coding	ENST00000321731	17	119075

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000273	0.999	125685	0	11	125696	0.0000438

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.218	273	263	1.04	0.0000122	3879
Missense in Polyphen		48	47.089	1.0193		661
Synonymous	-1.18	102	88.0	1.16	0.00000440	967
Loss of Function	2.95	15	33.4	0.449	0.00000155	493

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000127	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000548	0.0000528
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.000204	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Meiotic protein that localizes to the central element of the synaptonemal complex and is required for chromosome synapsis during meiotic recombination. Required for the appropriate processing of intermediate recombination nodules before crossover formation. {ECO:0000250|UniProtKB:Q9CTN5}.

Intolerance Scores

• rvis_EVS: 1.18
• rvis_percentile_EVS: 92.78

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.324

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 4930447C04Rik
• Phenotype: reproductive system phenotype; cellular phenotype; endocrine/exocrine gland phenotype