Is CFAP43 p.Arg1313Ter (c.3937C>T) pathogenic?

CFAP43 p.Arg1313Ter (c.3937C>T) is classified Likely pathogenic in CFAP43 (ClinVar, Single submitter, 1 submitter). Very rare (popmax 0.00453%, sas); Associated with normal pressure hydrocephalus.

What condition is associated with CFAP43 p.Arg1313Ter (c.3937C>T)?

CFAP43 p.Arg1313Ter (c.3937C>T) is associated with normal pressure hydrocephalus (ClinVar).

How common is CFAP43 p.Arg1313Ter (c.3937C>T) in the general population?

CFAP43 p.Arg1313Ter (c.3937C>T) is very rare (popmax 0.00453%, sas) (gnomAD).

CFAP43 p.Arg1313Ter

c.3937C>T · rs2087918488 · VCV2585282

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00453%, sas)

Conditions

normal pressure hydrocephalus

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 31 of 38
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.1	GERP -0.29, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00453% South Asian · 4/88,370 alleles

Filtering AF 0.00146% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000912%

Overall 0.000441% 7/1,588,722 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00453%	22,093
East Asian	0.00225%	44,420
European (non-Finnish)	0.000172%	580,970

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: CFAP43
Protein: p.Arg1313Ter
Coding: c.3937C>T
MANE Select: NM_025145
dbSNP: rs2087918488
Type: single nucleotide variant
Location: chr10:104145483 (GRCh38)
Gene constraint: LOEUF 0.78 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.27 · 1 PDB
Residue 1313: a UniProt-annotated variant site (in spgf19)

Full CFAP43 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

normal pressure hydrocephalus — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP43 p.Arg1313Gln Uncertain significance ★ ⚠ same residue
CFAP43 p.Thr1075Lys Uncertain significance ★★ ⚠ same condition
CFAP43 p.Cys44Ser Uncertain significance ★ ⚠ same condition
CFAP43 p.Val667Ile Conflicting classifications of pathogenicity ★ ⚠ same condition
CFAP43 p.Val905Ala Uncertain significance ★ ⚠ same condition
CFAP43 p.Trp1502Ter Pathogenic same condition
CFAP43 p.Thr1250fs Likely pathogenic ★★ same condition
CFAP43 p.Ser1527fs Likely pathogenic ★ 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/cfap43-p-arg1313ter (accessed [today's date]).

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