SEMA6C

protein-coding

semaphorin 6C, the group of Semaphorins

Gene summary

This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]

MANE transcript

NM_030913.6

Inheritance

—

ClinVar variants

U:23B:4

Top phenotype

SEMA6C-related condition

gnomAD constraint

pLI —, LoF o/e 0.42

Max pathogenic AF

—

Genomic locus

chr1:151,131,685-151,146,631

External References & Databases

Ensembl (ENSG00000143434)

Transcript & Mutation Effects

hg38 • Region Span ~14.9 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 SEMA6C variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 6

SEMA6C-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_030913.6. 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			2
missense			15 clinvar	2 clinvar	2 clinvar	19
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	23	2	2	27

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 81 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_030913.6	RefSeq	NP_112175.2	17	MANE Select
ENST00000368914.8	Ensembl	ENSP00000357910.3	17	MANE Select
NM_001178061.3	RefSeq	NP_001171532.1	18	Standard
NM_001178062.3	RefSeq	NP_001171533.1	17	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
axon guidance
positive regulation of cell migration
negative regulation of axon extension involved in axon guidance
negative chemotaxis

Molecular Function

semaphorin receptor binding
neuropilin binding
chemorepellent activity

Cellular Component

extracellular space
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368913
Coding exons: 18
Length: 14944
Individuals with no LoFs: 125632
Homozygous LoFs: 0
Heterozygous LoFs: 116
Defined: 125748
p: 0.000461

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.59	427	530	0.805	0.0000334	5992
Missense (PolyPhen)		73	93.577	0.7801		959
Synonymous	0.421	217	225	0.964	0.0000138	2169
Loss of Function	3.38	17	40.1	0.424	0.00000230	431

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00011	rare
Finnish	0.0034	0.0034	notable
European (Non-Finnish)	0.00025	0.00025	rare
South Asian	0.00026	0.00026	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Shows growth cone collapsing activity on dorsal root ganglion (DRG) neurons in vitro. May be a stop signal for the DRG neurons in their target areas, and possibly also for other neurons. May also be involved in the maintenance and remodeling of neuronal connections. {ECO:0000269|PubMed:12110693}.;

Recessive Scores

pRec: 0.100

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.132

Gene Damage Prediction

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