Genetic Variant STARD10:p.Cys181Tyr (chr11-72757801-GC-AT) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is The variant received 2 classification points (ACMG Germline Pathogenicity v2019). PM2

The NM_006645.3(STARD10):c.542_543delGCinsAT (p.Cys181Tyr) variant causes a missense change. Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.C181Y: Uncertain_significance (ClinVar VariationId 3170938, 1 star)

Frequency

Genomes: not found (cov: 33)

Consequence

STARD10
NM_006645.3 missense

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.36

Publications

0 publications found

Variant links:

Genes affected

STARD10 (HGNC:10666): (StAR related lipid transfer domain containing 10) Predicted to enable lipid carrier activity and phosphatidylcholine binding activity. Predicted to be involved in phosphatidylcholine biosynthetic process. Predicted to act upstream of or within bile acid secretion and positive regulation of peroxisome proliferator activated receptor signaling pathway. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

STARD10 links:

ARAP1 (HGNC:16925): (ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1) The protein encoded by this gene contains SAM, ARF-GAP, RHO-GAP, ankyrin repeat, RAS-associating, and pleckstrin homology (PH) domains. In vitro, this protein displays RHO-GAP and phosphatidylinositol (3,4,5) trisphosphate (PIP3)-dependent ARF-GAP activity. The encoded protein associates with the Golgi, and the ARF-GAP activity mediates changes in the Golgi and the formation of filopodia. It is thought to regulate the cell-specific trafficking of a receptor protein involved in apoptosis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

ARAP1 links:

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new If you want to explore the variant's impact on the transcript NM_006645.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Show applied only (1)

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Absent from gnomAD (AR/unknown gene) — PM2; Absent from gnomAD at well-covered site (MOI: unknown) (threshold 0.001) — PM2 moderate.

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_006645.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	STARD10 NM_006645.3	MANE Select	c.542_543delGCinsAT p.Cys181Tyr	missense	N/A	Prot: NP_006636.2 UniProt: Q9Y365

STARD10 NM_006645.3

MANE Select

HGVSc / HGVSpc.542_543delGCinsATp.Cys181Tyr

Exon rankN/A

missense

Prot: NP_006636.2UniProt: Q9Y365

Ensembl Transcripts

Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
STARD10 ENST00000334805.11	TSL:1MANE Select	c.542_543delGCinsAT p.Cys181Tyr	missense	N/A	Prot: ENSP00000335247.6 UniProt: Q9Y365
STARD10 ENST00000543304.5	TSL:1	c.542_543delGCinsAT p.Cys181Tyr	missense	N/A	Prot: ENSP00000438792.1 UniProt: Q9Y365
STARD10 ENST00000538536.5	TSL:1	c.404_405delGCinsAT p.Cys135Tyr	missense	N/A	Prot: ENSP00000440016.1 UniProt: F5GY11

STARD10 ENST00000334805.11

TSL:1MANE Select

HGVSc / HGVSpc.542_543delGCinsATp.Cys181Tyr

Exon rankN/A

missense

Prot: ENSP00000335247.6UniProt: Q9Y365

STARD10 ENST00000543304.5

TSL:1

HGVSc / HGVSpc.542_543delGCinsATp.Cys181Tyr

Exon rankN/A

missense

Prot: ENSP00000438792.1UniProt: Q9Y365

STARD10 ENST00000538536.5

TSL:1

HGVSc / HGVSpc.404_405delGCinsATp.Cys135Tyr

Exon rankN/A

missense

Prot: ENSP00000440016.1UniProt: F5GY11

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Benign	3.4

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational Scores

Splicing Scores

MaveDB functional evidence ?

Publications

Other links and lift over

MaveDB functional evidence