Is ESPN p.Lys660fs (c.1976_1977insCT) pathogenic?

ESPN p.Lys660fs (c.19761977insCT) is classified Likely pathogenic in ESPN (ClinVar, Single submitter, 1 submitter; last evaluated 2025-09-17). Associated with Usher syndrome, type 1M.

What condition is associated with ESPN p.Lys660fs (c.1976_1977insCT)?

ESPN p.Lys660fs (c.1976_1977insCT) is associated with Usher syndrome, type 1M, autosomal recessive nonsyndromic hearing loss 36 (ClinVar).

ESPN p.Lys660fs

c.1976_1977insCT · VCV4850343

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

Usher syndrome, type 1M

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 9 of 13
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

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

Variant & gene context

Gene: ESPN
Protein: p.Lys660fs
Coding: c.1976_1977insCT
MANE Select: NM_031475
Type: Insertion
Location: chr1:6451662 (GRCh38)
Gene constraint: LOEUF 1.307 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.76
Residue 660: the wh2 domain; the 'disordered' region

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

Disease context

Usher syndrome, type 1M — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive nonsyndromic hearing loss 36

Similar variants

ESPN p.Lys660Gln Uncertain significance ★ ⚠ same residue
ESPN c.1464+1G>A Likely pathogenic ★★ same condition
ESPN c.2339_2341del Uncertain significance ★★ same condition
ESPN p.Ala624Thr Uncertain significance ★★ ⚠ same condition
ESPN p.Arg755Cys Uncertain significance ★★ ⚠ same condition
ESPN p.Asp744Asn Uncertain significance ★★ ⚠ same condition
ESPN p.Gly747Ser Uncertain significance ★★ ⚠ same condition
ESPN p.Lys476Gln Uncertain significance ★★ ⚠ 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/espn-p-lys660fs (accessed [today's date]).

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