GCNA

germ cell nuclear acidic peptidase

Basic information

Region (hg38): X:71578437-71613583

Previous symbols: [ "ACRC" ]

Links

ENSG00000147174 ∙ NCBI:93953 ∙ OMIM:300369 ∙ HGNC:15805 ∙ Uniprot:Q96QF7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure, X-linked, 4	XL	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	33963445; 34413498; 35172124

ClinVar

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

• not_specified (95 variants)
• not_provided (10 variants)
• Spermatogenic_failure,_X-linked,_4 (4 variants)
• Non-obstructive_azoospermia (2 variants)
• Azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GCNA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052957.5. 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				5		5
missense	1		86	12		99
nonsense	1					1
start loss						0
frameshift	1	1				2
splice donor/acceptor (+/-2bp)						0
Total	3	1	86	17	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GCNA	protein_coding	protein_coding	ENST00000373695	12	35173

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.988	0.0121	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.745	247	282	0.875	0.0000245	4661
Missense in Polyphen		2	3.97	0.50377		66
Synonymous	0.691	118	128	0.922	0.0000139	1205
Loss of Function	3.68	1	17.7	0.0564	0.00000125	353

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

Recessive Scores

• pRec: 0.0604

Intolerance Scores

• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.0294
• hipred: N
• hipred_score: 0.360
• ghis: 0.382

Essentials

• essential_gene_gene_trap: N

Gene ontology

• Cellular component: nucleus