Is BLTP1 p.Arg3190Ter (c.9568C>T) pathogenic?

BLTP1 p.Arg3190Ter (c.9568C>T) is classified Likely pathogenic in BLTP1 (ClinVar, Single submitter, 2 submitters; last evaluated 2021-04-26). Very rare (popmax 0.00133%, afr); Associated with KIAA1109-related disorders.

What condition is associated with BLTP1 p.Arg3190Ter (c.9568C>T)?

BLTP1 p.Arg3190Ter (c.9568C>T) is associated with KIAA1109-related disorders (ClinVar).

How common is BLTP1 p.Arg3190Ter (c.9568C>T) in the general population?

BLTP1 p.Arg3190Ter (c.9568C>T) is very rare (popmax 0.00133%, afr) (gnomAD).

BLTP1 p.Arg3190Ter

c.9568C>T · rs1186567070 · VCV3045264

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

KIAA1109-related disorders

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 56 of 88
REVEL	0.066	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.4	GERP 1.4, phastCons 0.8
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 0.00133% African / African-American · 1/75,030 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000186% 3/1,613,910 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	75,030
European (non-Finnish)	0.00017%	589,946

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: BLTP1
Protein: p.Arg3190Ter
Coding: c.9568C>T
MANE Select: NM_001384125
dbSNP: rs1186567070
Type: single nucleotide variant
Location: chr4:122304879 (GRCh38)
Residue 3190: a UniProt-annotated variant site (in alkkucs)

Full BLTP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

KIAA1109-related disorders

Similar variants

BLTP1 p.Arg968Cys Likely pathogenic ★★ ⚠ same condition
BLTP1 p.His3063Arg Uncertain significance ★★ same condition
BLTP1 c.10312+2T>C Likely pathogenic ★ same condition
BLTP1 c.11513+1G>C Likely pathogenic ★ same condition
BLTP1 c.5184+1G>T Likely pathogenic ★ same condition
BLTP1 p.Phe3799Ser Uncertain significance ★ same condition
BLTP1 p.Val1878Ala Uncertain significance ⚠ same condition
BLTP1 c.6378+10T>C Benign 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/bltp1-p-arg3190ter (accessed [today's date]).

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