Is CLCC1 p.Ser156fs (c.464dup) pathogenic?

CLCC1 p.Ser156fs (c.464dup) is classified Uncertain significance in CLCC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-10-11). Absent from gnomAD.

How common is CLCC1 p.Ser156fs (c.464dup) in the general population?

CLCC1 p.Ser156fs (c.464dup) is absent from gnomAD (gnomAD).

CLCC1 p.Ser156fs

c.464dup · rs1557894863 · VCV1488409

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 6 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2.8	GERP -3.5

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CLCC1
Protein: p.Ser156fs
Coding: c.464dup
MANE Select: NM_001377458
dbSNP: rs1557894863
Type: Duplication
Location: chr1:108943932 (GRCh38)
Gene constraint: LOEUF 0.778 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.13

Full CLCC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CLCC1 p.Ser156Gly Benign ★★ same residue
CLCC1 p.Thr407fs Uncertain significance ★ same type
GPSM2 p.His684_Ter685= Uncertain significance ★ same type
GPSM2 p.Ser681fs Uncertain significance ★ same type
CLCC1 c.129+13dup Benign ★ same type
CLCC1 c.1384-8_1384-4dup Likely benign ★ same type
CLCC1 c.231+12dup Benign ★ same type
CLCC1 c.340-17dup Benign ★ same type

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/clcc1-p-ser156fs (accessed [today's date]).

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