SEMA4F

protein-coding

ssemaphorin 4F, the group of Semaphorins

Gene summary

This gene encodes a transmembrane class IV semaphorin family protein, which plays a role in neural development. This gene may be involved in neurogenesis in prostate cancer, the development of neurofibromas, and breast cancer tumorigenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

Previous symbols:

SEMAM

MANE transcript

NM_004263.5

Inheritance

—

ClinVar variants

U:132B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr2:74,654,226-74,690,634

External References & Databases

Ensembl (ENSG00000135622)

Transcript & Mutation Effects

hg38 • Region Span ~36.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SEMA4F variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 133

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004263.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	1 clinvar		3
missense			127 clinvar	8 clinvar		135
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	132	9	0	141

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 44 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004263.5	RefSeq	NP_004254.2	14	MANE Select
ENST00000357877.7	Ensembl	ENSP00000350547.2	14	MANE Select
NM_001271661.2	RefSeq	NP_001258590.1	10	Standard
NM_001271662.2	RefSeq	NP_001258591.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Axon guidance - Homo sapiens (human)

Biological Process

neural crest cell migration
cell-cell signaling
nervous system development
axon guidance
positive regulation of cell migration

Molecular Function

semaphorin receptor binding
neuropilin binding
chemorepellent activity

Cellular Component

extracellular space
endoplasmic reticulum
plasma membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000357877
Coding exons: 14
Length: 27832
Individuals with no LoFs: 125575
Homozygous LoFs: 0
Heterozygous LoFs: 173
Defined: 125748
p: 0.000688

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.322	451	471	0.958	0.0000293	4899
Missense (PolyPhen)		151	169.07	0.89311		1891
Synonymous	-0.261	190	185	1.02	0.0000107	1701
Loss of Function	1.96	25	38.0	0.658	0.00000240	373

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0014	0.0013	notable
Latino/Admixed American	0.00093	0.00093	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00065	0.00065	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00085	0.00084	rare
South Asian	0.00020	0.00020	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Has growth cone collapse activity against retinal ganglion-cell axons. {ECO:0000250}.;

Recessive Scores

pRec: 0.0945

Intolerance Scores

LoFtool: 0.860
RVIS EVS: -1.06
RVIS percentile EVS: 7.52

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.149

Gene Damage Prediction

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