SFT2D1

protein-coding

SFT2 domain containing 1

Gene summary

Predicted to be involved in protein transport and vesicle-mediated transport. Predicted to be located in cytoplasm; endomembrane system; and membrane. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C6orf83

MANE transcript

NM_145169.3

Inheritance

—

ClinVar variants

U:28B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.54

Max pathogenic AF

—

Genomic locus

chr6:166,319,728-166,342,576

External References & Databases

Ensembl (ENSG00000198818)

Transcript & Mutation Effects

hg38 • Region Span ~22.8 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 SFT2D1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 20

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145169.3. 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						0
missense			19 clinvar	2 clinvar		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			9 clinvar			9
Total	0	0	28	2	0	30

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145169.3	RefSeq	NP_660152.1	8	MANE Select
ENST00000361731.4	Ensembl	ENSP00000354590.3	8	MANE Select
ENST00000866111.1	Ensembl	ENSP00000536170.1	7	Standard
ENST00000866111.2	Ensembl	ENSP00000536170.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

protein transport
vesicle-mediated transport

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361731
Coding exons: 8
Length: 22864
Individuals with no LoFs: 125716
Homozygous LoFs: 0
Heterozygous LoFs: 30
Defined: 125746
p: 0.000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.313	72	79.9	0.902	0.00000388	1012
Missense (PolyPhen)		8	14.429	0.55446		196
Synonymous	-0.598	37	32.7	1.13	0.00000187	296
Loss of Function	1.42	6	11.1	0.540	4.71e-7	138

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00012	rare
Latino/Admixed American	0.000059	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00083	0.00082	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000037	0.000035	rare
South Asian	0.00013	0.00013	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with the Golgi complex. {ECO:0000250|UniProtKB:P38166}.;

Recessive Scores

pRec: 0.0651

Intolerance Scores

RVIS EVS: 0.1
RVIS percentile EVS: 61.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.519

Gene Damage Prediction

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