Is DLC1 p.Gln155= (c.465A>G) pathogenic?

DLC1 p.Gln155= (c.465A>G) is classified Uncertain significance in DLC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-12). Ultra-rare (popmax 0.024%, afr); Associated with colorectal cancer.

What condition is associated with DLC1 p.Gln155= (c.465A>G)?

DLC1 p.Gln155= (c.465A>G) is associated with colorectal cancer (ClinVar).

How common is DLC1 p.Gln155= (c.465A>G) in the general population?

DLC1 p.Gln155= (c.465A>G) is ultra-rare (popmax 0.024%, afr) (gnomAD).

DLC1 p.Gln155=

c.465A>G · VCV3595233

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.024%, afr)

Conditions

colorectal cancer

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.12	GERP -3.9, phastCons 0.077
Overall
CADD	0.583	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.024% African / African-American · 18/74,928 alleles

Filtering AF 0.0155% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0128%

Overall 0.00118% 19/1,614,018 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.024%	4,163
European (non-Finnish)	8.47e-05%	1,180,006

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: DLC1
Protein: p.Gln155=
Coding: c.465A>G
MANE Select: NM_003746 · reported on NM_182643
Type: single nucleotide variant
Location: chr8:13499607 (GRCh38)
Structure: AlphaFold pLDDT 95.45 · 22 PDB

Full DLC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

colorectal cancer — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

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DLC1 p.Ala350Val Uncertain significance ★★ ⚠ same condition
DLC1 p.Ala821Val Uncertain significance ★★ ⚠ same condition
DLC1 p.Arg1073Trp Uncertain significance ★★ ⚠ same condition
DLC1 p.Arg1126Cys Uncertain significance ★★ ⚠ same condition
DLC1 p.Arg1182Cys Uncertain significance ★★ ⚠ same condition
DLC1 p.Arg1182His Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dlc1-p-gln155 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown