Is CEP85L p.His387Arg (c.1160A>G) pathogenic?

CEP85L p.His387Arg (c.1160A>G) is classified Likely benign in CEP85L (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-11). AlphaMissense: likely benign (0.1533); Ultra-rare (popmax 0.0201%, eas); Associated with Inborn genetic diseases.

What condition is associated with CEP85L p.His387Arg (c.1160A>G)?

CEP85L p.His387Arg (c.1160A>G) is associated with Inborn genetic diseases (ClinVar).

How common is CEP85L p.His387Arg (c.1160A>G) in the general population?

CEP85L p.His387Arg (c.1160A>G) is ultra-rare (popmax 0.0201%, eas) (gnomAD).

What do computational predictors say about CEP85L p.His387Arg (c.1160A>G)?

AlphaMissense predicts likely benign (score 0.1533) — an in-silico prediction, not a clinical call.

CEP85L p.His387Arg

c.1160A>G · VCV3266282

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1533 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0201%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1533	likely benign
REVEL	0.026	moderately benign-leaning
SaProt	LLR -5.27	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 6.1	GERP 1.6, phastCons 1
Regional constraint	o/e 1.05	unconstrained · MANE · 167 kb · p 0.12 · regional, not allelic
Overall
CADD	20.3	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 0.0201% East Asian · 9/44,828 alleles

Filtering AF 0.0104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0078%

Overall 0.000682% 11/1,611,874 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0201%	4,981
Remaining individualsnot grpmax-eligible	0.00321%	31,191

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: CEP85L
Protein: p.His387Arg
Coding: c.1160A>G
MANE Select: NM_001042475
Type: single nucleotide variant
Location: chr6:118511395 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 64.98

Full CEP85L gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CEP85L p.Arg151Gln Uncertain significance ★★ ⚠ same condition
CEP85L p.Arg241Ser Uncertain significance ★★ ⚠ same condition
CEP85L p.Gly122Ser Uncertain significance ★★ ⚠ same condition
CEP85L p.Ile186Val Uncertain significance ★★ ⚠ same condition
CEP85L p.Pro152Ala Uncertain significance ★★ ⚠ same condition
CEP85L p.Ser262Gly Uncertain significance ★★ ⚠ same condition
CEP85L p.Thr66Ile Uncertain significance ★★ ⚠ same condition
CEP85L p.Lys220Thr Likely 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/cep85l-p-his387arg (accessed [today's date]).

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