HFM1

helicase for meiosis 1, the group of RNA helicases

Basic information

Region (hg38): 1:91260766-91404856

Previous symbols: [ "SEC63D1" ]

Links

ENSG00000162669

∙ NCBI:164045 ∙ OMIM:615684 ∙ HGNC:20193 ∙ Uniprot:A2PYH4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

male infertility with azoospermia or oligozoospermia due to single gene mutation (Disputed Evidence), mode of inheritance: AR
premature ovarian failure 9 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Premature ovarian failure 9	AR	Obstetric	Genetic knowledge may be beneficial to allow interventions such as preserving eggs in women with premature ovarian insufficiency	Endocrine; Obstetric	24597873

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HFM1 gene.

not_specified (155 variants)
Premature_ovarian_failure_9 (15 variants)
not_provided (11 variants)
HFM1-related_disorder (9 variants)
Spermatogenic_failure_4 (2 variants)
Genetic_non-acquired_premature_ovarian_failure (2 variants)
Azoospermia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HFM1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001017975.6. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous	1 clinvar		1 clinvar	4 clinvar	1 clinvar	7
missense	5 clinvar	1 clinvar	143 clinvar	13 clinvar	4 clinvar	166
nonsense	1 clinvar	1 clinvar	1 clinvar			3
start loss		1				1
frameshift	1 clinvar	2 clinvar	4 clinvar			7
splice donor/acceptor (+/-2bp)	2 clinvar	2 clinvar				4
Total	10	7	149	17	5

Highest pathogenic variant AF is 0.0000751985

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HFM1	protein_coding	protein_coding	ENST00000370425	38	144104

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.73e-32	0.0809	125603	0	137	125740	0.000545

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.742	627	682	0.920	0.0000319	9464
Missense in Polyphen		142	181.84	0.78089		2547
Synonymous	0.593	215	226	0.950	0.0000105	2551
Loss of Function	2.07	60	80.0	0.750	0.00000415	1083

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000768	0.000755
Ashkenazi Jewish	0.00	0.00
East Asian	0.000638	0.000598
Finnish	0.000696	0.000693
European (Non-Finnish)	0.000730	0.000704
Middle Eastern	0.000638	0.000598
South Asian	0.000407	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Required for crossover formation and complete synapsis of homologous chromosomes during meiosis. {ECO:0000250|UniProtKB:D3Z4R1}.;

Intolerance Scores

loftool: 0.986
rvis_EVS: -0.72
rvis_percentile_EVS: 14.27

Haploinsufficiency Scores

pHI: 0.0728
hipred: N
hipred_score: 0.307
ghis: 0.490

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.177

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Hfm1
Phenotype: endocrine/exocrine gland phenotype; reproductive system phenotype;

Gene ontology

Biological process: resolution of meiotic recombination intermediates
Cellular component
Molecular function: nucleic acid binding;helicase activity;ATP binding