EFNA1

Chr 1

ephrin A1

Also known as: B61, ECKLG, EPLG1, GMAN, LERK-1, LERK1, TNFAIP4

NCBI Gene: 1942 ENSG00000169242 OMIM: 191164

This gene encodes a member of the ephrin (EPH) family. The ephrins and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, especially in the nervous system and in erythropoiesis. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. This gene encodes an EFNA class ephrin which binds to the EPHA2, EPHA4, EPHA5, EPHA6, and EPHA7 receptors. Two transcript variants that encode different isoforms were identified through sequence analysis. [provided by RefSeq, Jul 2008]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOEUF 0.63

Clinical Summary— EFNA1

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.20) despite low pLI — interpret in context.

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ClinVar Variants

20 VUS of 28 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.63LOEUF

pLI 0.463

Z-score 2.34

OE 0.20 (0.08–0.63)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.83Z-score

OE missense 0.79 (0.67–0.93)

96 obs / 121.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.20 (0.08–0.63)

0≤0.351.4

Missense OE?0.79 (0.67–0.93)

0≤0.61.4

Synonymous OE?0.81

0≤1.21.6

LoF obs/exp: 2 / 10.0Missense obs/exp: 96 / 121.9Syn Z: 1.04

ClinVar Variant Classifications

28 submitted variants in ClinVar

ClinVar

Classification Summary

VUS20

Likely Benign1

Benign1

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Total
Pathogenic	0	0
Likely Pathogenic	0	0
VUS	20	20
Likely Benign	1	1
Benign	1	1
Total	22	22

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

14 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap EFNA1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →