NM_178006.4:c.3076A>C

Variant names:

• chr13-33106906-T-G
• NM_178006.4:c.3076A>C

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_178006.4(STARD13):​c.3076A>C​(p.Met1026Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: STARD13 NM_178006.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.98
• Publications: 0 publications found

Genes affected

STARD13 (HGNC:19164): (StAR related lipid transfer domain containing 13) This gene encodes a protein which contains an N-terminal sterile alpha motif (SAM) for protein-protein interactions, followed by an ATP/GTP-binding motif, a GTPase-activating protein (GAP) domain, and a C-terminal STAR-related lipid transfer (START) domain. It may be involved in regulation of cytoskeletal reorganization, cell proliferation, and cell motility, and acts as a tumor suppressor in hepatoma cells. The gene is located in a region of chromosome 13 that is associated with loss of heterozygosity in hepatocellular carcinomas. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]

STARD13 Gene-Disease associations (from GenCC):

• schizophrenia

  Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33408836).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STARD13	NM_178006.4	c.3076A>C	p.Met1026Leu	missense_variant	Exon 13 of 14	ENST00000336934.10	NP_821074.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STARD13	ENST00000336934.10	c.3076A>C	p.Met1026Leu	missense_variant	Exon 13 of 14	1	NM_178006.4	ENSP00000338785.4
STARD13	ENST00000255486.8	c.3052A>C	p.Met1018Leu	missense_variant	Exon 13 of 14	1		ENSP00000255486.4
STARD13	ENST00000567873.2	c.3031A>C	p.Met1011Leu	missense_variant	Exon 13 of 14	1		ENSP00000456233.2
STARD13	ENST00000399365.7	c.2722A>C	p.Met908Leu	missense_variant	Exon 13 of 14	1		ENSP00000382300.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Apr 29, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.3076A>C (p.M1026L) alteration is located in exon 13 (coding exon 13) of the STARD13 gene. This alteration results from a A to C substitution at nucleotide position 3076, causing the methionine (M) at amino acid position 1026 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.15
BayesDel_addAF	Benign	-0.036	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Benign	0.97
DEOGEN2	Benign	0.078	T;.;.
Eigen	Benign	-0.35
Eigen_PC	Benign	-0.16
FATHMM_MKL	Benign	0.44	N
LIST_S2	Benign	0.84	T;T;T
M_CAP	Benign	0.018	T
MetaRNN	Benign	0.33	T;T;T
MetaSVM	Benign	-0.71	T
MutationAssessor	Benign	0.34	N;.;.
PhyloP100		2.0
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-0.48	N;N;N
REVEL	Benign	0.26
Sift	Benign	0.041	D;D;D
Sift4G	Uncertain	0.040	D;D;D
Polyphen		0.0080	B;B;.
Vest4		0.42
MutPred		0.46		Gain of catalytic residue at M1026 (P = 0.0286);.;.;
MVP		0.72
MPC		0.13
ClinPred		0.38	T
GERP RS		6.0
Varity_R		0.31
gMVP		0.34
Mutation Taster		=88/12	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

hg19: chr13-33681043;