Is CFAP144 p.Thr125Met (c.374C>T) pathogenic?

CFAP144 p.Thr125Met (c.374C>T) is classified Likely benign in CFAP144 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-09). AlphaMissense: likely benign (0.0532); Ultra-rare (popmax 0.024%, afr).

How common is CFAP144 p.Thr125Met (c.374C>T) in the general population?

CFAP144 p.Thr125Met (c.374C>T) is ultra-rare (popmax 0.024%, afr) (gnomAD).

What do computational predictors say about CFAP144 p.Thr125Met (c.374C>T)?

AlphaMissense predicts likely benign (score 0.0532) — an in-silico prediction, not a clinical call.

CFAP144 p.Thr125Met

c.374C>T · VCV3832239

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0532 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.024%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0532	likely benign
REVEL	0.025	moderately benign-leaning
SaProt	LLR -3.40	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.37	GERP -0.45, phastCons 0.21
Regional constraint	o/e 0.91	unconstrained · MANE · 8,358 bp · p 0.24 · regional, not allelic
Overall
CADD	7.762	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.024% African / African-American · 18/74,926 alleles

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

Overall 0.00384% 62/1,613,862 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.024%	4,163
Admixed American	0.00833%	12,002
Remaining individualsnot grpmax-eligible	0.0032%	31,230
European (non-Finnish)	0.00314%	31,888

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: CFAP144
Protein: p.Thr125Met
Coding: c.374C>T
MANE Select: NM_001101376
Type: single nucleotide variant
Location: chr1:43156282 (GRCh38)
Structure: AlphaFold pLDDT 79.41 · 2 PDB

Full CFAP144 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP144 p.Arg104Cys Uncertain significance ★ ⚠ same type
CFAP144 p.Asp130Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Asp57Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Asp64Asn Uncertain significance ★ ⚠ same type
CFAP144 p.Glu60Gly Uncertain significance ★ ⚠ same type
CFAP144 p.Gly129Val Uncertain significance ★ ⚠ same type
CFAP144 p.His56Tyr Uncertain significance ★ ⚠ same type
CFAP144 p.Ile100Val Conflicting classifications of pathogenicity ★ ⚠ 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/cfap144-p-thr125met (accessed [today's date]).

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