Is CCDC159 p.Thr183Met (c.548C>T) pathogenic?

CCDC159 p.Thr183Met (c.548C>T) is classified Uncertain significance in CCDC159 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-07). AlphaMissense: likely benign (0.1454); Very rare (popmax 0.00834%, amr).

How common is CCDC159 p.Thr183Met (c.548C>T) in the general population?

CCDC159 p.Thr183Met (c.548C>T) is very rare (popmax 0.00834%, amr) (gnomAD).

What do computational predictors say about CCDC159 p.Thr183Met (c.548C>T)?

AlphaMissense predicts likely benign (score 0.1454) — an in-silico prediction, not a clinical call.

CCDC159 p.Thr183Met

c.548C>T · VCV3996659

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1454 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00834%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1454	likely benign
REVEL	0.053	moderately benign-leaning
SaProt	LLR -6.85	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.48 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.2	GERP 0.056, phastCons 0.65
Regional constraint	o/e 0.96	unconstrained · MANE · 8,267 bp · p 0.42 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00834% Admixed American · 5/59,970 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.00167% 27/1,613,498 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00834%	11,994
African / African-American	0.00401%	24,944
Remaining individualsnot grpmax-eligible	0.0032%	31,229
East Asian	0.00223%	44,880
South Asian	0.0022%	45,536
European (non-Finnish)	0.00119%	84,272

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: CCDC159
Protein: p.Thr183Met
Coding: c.548C>T
MANE Select: NM_001080503
Type: single nucleotide variant
Location: chr19:11352114 (GRCh38)
Gene constraint: LOEUF 1.11 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.97

Full CCDC159 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CCDC159 p.Ala203Thr Uncertain significance ★ ⚠ same type
CCDC159 p.Ala45Asp Uncertain significance ★ ⚠ same type
CCDC159 p.Arg117Cys Uncertain significance ★ ⚠ same type
CCDC159 p.Arg117His Uncertain significance ★ ⚠ same type
CCDC159 p.Arg124Trp Uncertain significance ★ ⚠ same type
CCDC159 p.Arg126Gly Uncertain significance ★ ⚠ same type
CCDC159 p.Arg139Gln Uncertain significance ★ ⚠ same type
CCDC159 p.Arg139Trp Uncertain significance ★ ⚠ 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/ccdc159-p-thr183met (accessed [today's date]).

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