Is IFT43 p.Arg12= (c.36C>T) pathogenic?

IFT43 p.Arg12= (c.36C>T) is classified Likely benign in IFT43 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-23). Very rare (popmax 0.00223%, eas).

How common is IFT43 p.Arg12= (c.36C>T) in the general population?

IFT43 p.Arg12= (c.36C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

IFT43 p.Arg12=

c.36C>T · rs779037618 · VCV1957018

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.90 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.038	GERP -1.8, phastCons 0.79
Overall
CADD	5.158	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,884 alleles

Overall 0.000124% 2/1,614,064 alleles · very rare exomes 1/1,461,860 · genomes 1/152,204 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,884
European (non-Finnish)	8.47e-05%	1,180,038

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: IFT43
Protein: p.Arg12=
Coding: c.36C>T
MANE Select: NM_001102564
dbSNP: rs779037618
Type: single nucleotide variant
Location: chr14:75985822 (GRCh38)
Gene constraint: LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.09 · 3 PDB

Full IFT43 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

IFT43 p.Arg12Cys Uncertain significance ★★ ⚠ same residue
IFT43 p.Arg12Ser Uncertain significance ★★ ⚠ same residue
IFT43 c.148-2A>C Likely pathogenic ★★ same type
IFT43 c.296-5698C>T Likely pathogenic ★★ same type
IFT43 c.296-5681A>G Uncertain significance ★★ same type
IFT43 c.296-5697G>A Uncertain significance ★★ same type
IFT43 c.444+5G>A Uncertain significance ★★ same type
IFT43 p.Ala162Thr 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/ift43-p-arg12 (accessed [today's date]).

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